Protein Data Bank Contents Guide:

Atomic Coordinate Entry Format Description

Version 2.1 (draft), October 25, 1996




Preface

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data.

Entries conforming to this format description have the following remark within them:

       REMARK   4 XXXX COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996

Entries released after October 25, 1996 will comply with this format. Conversion of older entries to this format will begin in the fall of 1996.

This Contents Guide was prepared through the efforts of all PDB staff members: J. Callaway, M. Cummings, B. Deroski, P. Esposito, A. Forman, P. Langdon, M. Libeson, J. McCarthy, J. Sikora, D. Xue; and especially E. Abola, F. Bernstein, N. Manning, R. Shea, D. Stampf, and J. Sussman. This document also included significant contributions from the scientific community whose members continually send us suggestions and comments regarding the contents and format of PDB entries.

Please send any comments or suggestions on this Contents Guide to the PDB Help Desk.

   Protein Data Bank Help Desk        E-mail: pdbhelp@bnl.gov 
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The PDB is supported by a combination of Federal Government Agency funds and user fees. Support is provided by the U.S. National Science Foundation, the U.S. Public Health Service, National Institutes of Health, National Center for Research Resources, National Institutes of General Medical Sciences, National Library of Medicine, and the U.S. Department of Energy under contract DE-AC02-76CH00016.



Table of Contents

Preface

Table of Contents

1. Introduction

Purpose of this Document
What's New in Version 2.1
What's New in Version 2.0
Changes to PDB Format 2.0 Being Proposed on October 25, 1996
Changes to PDB Format and to the Contents Guide
Basic Notions of the Format Description
Record Format
Types of Records
Order of Records
Field Formats

2. Title Section

HEADER
OBSLTE
TITLE
CAVEAT
COMPND
SOURCE
KEYWDS
EXPDTA
AUTHOR
REVDAT
SPRSDE
JRNL
REMARK
REMARK 1
REMARK 2
REMARK 3
REMARK 4 - 999

3. Primary Structure Section

DBREF
SEQADV
SEQRES
MODRES

4. Heterogen Section

HET
HETNAM
HETSYN
FORMUL

5. Secondary Structure Section

HELIX
SHEET
TURN

6. Connectivity Annotation Section

SSBOND
LINK
HYDBND
SLTBRG
CISPEP

7. Miscellaneous Features Section

SITE

8. Crystallographic and Coordinate Transformation Section

CRYST1
ORIGXn
SCALEn
MTRIXn
TVECT

9. Coordinate Section

MODEL
ATOM
SIGATM
ANISOU
SIGUIJ
TER
HETATM
ENDMDL

10. Connectivity Section

CONECT

11. Bookkeeping Section

MASTER
END

Appendix 1: Symmetry Operations

Appendix 2: Coordinate Systems and Transformations

Appendix 3: Atom Names

Amino Acids
Nucleic Acids

Appendix 4: Standard Residue Names and Abbreviations

Amino Acids
Nucleic Acids

Appendix 5: Formulas and Molecular Weights For Standard Residues

Amino Acids
Nucleotides

Appendix 6: Field Formats

Appendix 7: Order of Records



1. Introduction

Purpose of this Document

The PDB Contents Guide gives a complete and concise description of the contents of PDB coordinate entry files. This document will be helpful to several communities, assisting depositors in preparing their entries for deposition, guiding software and information resource developers, and helping users of PDB to understand the contents of coordinate entries. Finally, this format description is crucial in the effort to produce CIF-compliant data files from PDB entries.

What's New in Version 2.1

List of changes/enhancements to PDB format as found in Contents Guide Version 2.1.

* MODRES records appear immediately following SEQRES. (The order was incorrectly stated in Version 2.0.)
* REMARK 3 has a new X-PLOR template to reflect the changes introduced by the recent release of X-PLOR(online)3.843.
* REMARK 3 will use the word NONE (for the attribute in the value-attribute pair) when the attribute is not applicable or when analysis options were chosen such that a value was not calculated. NULL will continue to be used to represent values not supplied by the depositor.
* COMPND and SOURCE have a few additional tokens.
* Some examples are enhanced, a few have been added.
* Language of the text has been improved in some places to help clarify the format.

What's New in Version 2.0

List of important changes/enhancements to PDB format as found in Contents Guide Version 2.0.

* Columns 71 - 80 now contain data. They previously contained the PDB ID code and record serial number. These items may be generated using scripts available from the PDB.

Changes to ATOM/HETATM Records

* A segment identifier has been added to the coordinate records in columns 73 - 76. This allows unambiguous identification of regions of the chains and the relationship between them by specifying segments of molecules.
* The element symbol and charge now appear in columns 77 - 80 of the coordinate records.
* When temperature factors are provided, the tempFactor field (columns 61 - 66) always contains the isotropic B value, even when ANISOU records are provided.
* Insertion codes (column 27) are now defined as being alphabetic only.

Changes to Other Records

* HELIX records now contain the length of the helix in columns 72 - 76.
* SSBOND records now state the symmetry operation needed to generate one of the residues of the disulfide bond, if necessary.
* Footnotes (FTNOTE) have been dropped.
* In CRYST1 records:
         - The full international Hermann-Mauguin symbol is used, 
           e.g., P 1 21 1 instead of P 21. 

         - For a rhombohedral space group in the hexagonal setting, 
           the lattice type symbol used is H.

* A number of record types which previously contained free text have been restructured as follows:
         - "Keyword: value" pairs have been introduced in certain records   
           such as COMPND and SOURCE to allow easier parsing.

         - EXPDTA has been expanded and now appears in every PDB coordinate 
           entry.

         - REMARK records have been restructured to allow easier parsing    
           and to bring more organization to these records.

New Record Types Added

* TITLE
* CAVEAT
* KEYWDS
* MODRES
* DBREF
* SEQADV
* HETNAM
* HETSYN
* LINK
* HYDBND
* SLTBRG
* CISPEP

For details on each of these changes, see the section of the associated record type in this document.

Changes to PDB Format 2.0 Being Proposed on October 25, 1996

A number of changes are being proposed to the existing data format. We are presenting these changes here for consideration. In accordance with PDB's Format Change Policy (http://www.pdb.bnl.gov/format_change_policy.html), there will be an open sixty-day discussion period during which we will entertain comments and suggestions regarding these changes. Send comments to Enrique Abola (abola1@bnl.gov) or to Nancy Manning (oeder@bnl.gov). Discussion on the PDB Listserver is encouraged as well.

Changes being proposed here, if adopted, will not appear in released entries before March 31, 1997. A public announcement will be made some weeks prior to their appearance in released entries.

1. Hydrogen Atom Names in Amino Acids

Methylene hydrogen atoms will be labeled as 2HX and 3HX where X is the remoteness indicator of the atom. For example, hydrogen atoms attached to C beta of an amino acid will be named 2HB and 3HB. Our current convention is to name these 1HB and 2HB. This change will make PDB more compliant with IUPAC recommendations.

2. Space Group Symbol for Monoclinic Crystals

The use of the shortened Hermann-Mauguin symbol for monoclinic crystals will be reinstated. This will be applied to crystals in the standard b-unique cell setting. Thus the space group symbol P 21 will be used instead of P  1  21  1. Crystals using other settings will be designated with the full international Hermann-Mauguin symbol (e.g., P  21  1  1).

3. Representation of Modified Nucleic Acid Residues

Modified nucleic acids will be represented using the same rules that are used by the PDB for representing modified amino acids. We will assign a unique three-letter code for modified residues. For example, we will use BRU for brominated uridine rather than +U. In addition, all atoms belonging to the residue will be grouped together in the coordinate records. Our current practice is to list atoms that modify nucleotides after the TER record.

Changes to PDB Format and to the Contents Guide

When a change is made to PDB format, the format version number, as found in the entry and in this Contents Guide, will be incremented to the next whole number. Changes to the format of PDB coordinate entry files will follow the Format Change Policy presented below and will be detailed in this Contents Guide. Beginning January 1997, the format of all PDB entries will be compliant with the current version of this Contents Guide.

Changes to the Contents Guide will be listed at the beginning in the What's New section and denoted by a fractional increase in the document version number. These changes may be of the following kind.

* Correction of typographical errors.
* Changes to the language for clarity.
* Addition or changes to the examples for better representation of format issues.
* Addition of new rules (these do not change the format but help to clarify the semantics).
* Addition of tokens to specification lists, such as in COMPND and SOURCE records, that are needed to more fully describe the structure and its biological source.
* Enhancements to the refinement and experimental details templates in the REMARK records. These remarks are currently being reviewed by several people in the community, and PDB expects to increase the level of detail archived, such as for NMR studies.
* Addition of new sections that enhance and expand the document (these may include topics such as PDB to mmCIF cross references or insertion of relevant sections from the PDB Deposition Form).

Format Change Policy

The PDB will use the following protocol in making changes to the way PDB coordinate entries are represented and archived. The purpose of the new policy is to allow ample time for everyone to understand these changes and to assess their impact on existing programs. These modifications are necessary to address the changing needs of our users as well as the changing nature of the data that is archived.

1. Comments and suggestions will be solicited from the community on specific problems and data representation issues as they arise.
2. Proposed format changes will be disseminated through the PDB Listserver (pdb-l@pdb.pdb.bnl.gov) and PDB's Internet sites (WWW, FTP, and Gopher). They will also be summarized in the PDB Quarterly Newsletter.
3. A sixty-day discussion period will follow the announcement of proposed changes. Comments and suggestions must be received within this time period. Major changes which are not upwardly compatible will be allotted up to twice the standard amount of discussion time.
4. This sixty-day discussion period will be followed by a thirty-day period in which the PDB staff, the PDB Advisory Board, and the User Group Chair will evaluate and reconcile all suggestions. The final decision pertaining to the format change, which lies with the Advisory Board Chair, will then be officially announced via the PDB Listserver and PDB's Internet sites (WWW, FTP, and Gopher).
5. Implementation will follow official announcement of the format change. Major changes will not appear in PDB files earlier than sixty days after the announcement, allowing sufficient time to modify files and programs.
6. Changes will be released no more than twice a year, unless extraordinary circumstances require action. This will be done only in consultation with the Advisory Board and following the usual ninety-day discussion and evaluation period.

The PDB format has been in use since the late 1970's. A number of groups including the mmCIF Committee have been looking at ways to upgrade both the file content and the interchange format used by PDB. This is clearly needed due to changes in the data that PDB archives, the size of the database itself, and finally, to allow PDB to use more up-to-date methods for representing and storing biological data.

The PDB plans to be prudent and deliberate in making changes to the current PDB files in order to minimize the need to change existing programs. In particular, we will explore ways and means of ensuring that programs which read the current ATOM/HETATM records can continue to do so in the foreseeable future.

The PDB wishes to acknowledge Dr. Gerald Selzer of the National Science Foundation who urged us to formulate this policy.

Basic Notions of the Format Description

Character Set

Only non-control ASCII characters, as well as the space and end-of-line indicator, appear in a PDB coordinate entry file. Namely:

abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ

1234567890

` - = [ ] \ ; ' , . / ~ ! @ # $ % ^ & * ( ) _ + { } | : " < > ?

the space, and end-of-line. The end-of-line indicator is system-specific. Unix uses a line feed character; other systems may use a carriage return followed by a line feed.

Special Characters

Greek letters are spelled out, i.e., alpha, beta, gamma, etc.

Bullets are represented as (DOT).

Right arrow is represented as -->.

Left arrow is represented as <--.

Superscripts are initiated and terminated by double equal signs, e.g., S==2+==.

Subscripts are initiated and terminated by single equal signs, e.g., F=c=.

If "=" is surrounded by at least one space on each side, then it is assumed to be an equal sign, e.g., 2 + 4 = 6.

Commas, colons, and semi-colons are used as list delimiters in records which have one of the following data types:

List
SList
Specification List
Specification

If a comma, colon, or semi-colon is used in any context other than as a delimiting character, then the character must be escaped, i.e., immediately preceded by a backslash, "\". Examples of this use are found in line 4 of each of the following:

COMPND    MOL_ID: 1;                                                       
COMPND   2 MOLECULE: GLUTATHIONE SYNTHETASE;                               
COMPND   3 CHAIN: NULL; 
COMPND   4 SYNONYM: GAMMA-L-GLUTAMYL-L-CYSTEINE\:GLYCINE LIGASE            
COMPND   5 (ADP-FORMING);                                                  
COMPND   6 EC: 6.3.2.3;                                                    
COMPND   7 ENGINEERED: YES                                                 

COMPND    MOL_ID: 1;                                                       
COMPND   2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHETASE;                      
COMPND   3 CHAIN: A, B;                                                    
COMPND   4 SYNONYM: MAT, ATP\:L-METHIONINE S-ADENOSYLTRANSFERASE;      
COMPND   5 EC: 2.5.1.6;                                                    
COMPND   6 ENGINEERED: YES;                                                
COMPND   7 BIOLOGICAL_UNIT: TETRAMER;                                      
COMPND   8 OTHER_DETAILS: TETRAGONAL MODIFICATION                          

Record Format

Every PDB file may be broken into a number of lines terminated by an end-of-line indicator. Each line in the PDB entry file consists of 80 columns. The last character in each PDB entry should be an end-of-line indicator.

Each line in the PDB file is self-identifying. The first six columns of every line contain a record name, left-justified and blank-filled. This must be an exact match to one of the stated record names.

The PDB file may also be viewed as a collection of record types. Each record type consists of one or more lines.

Each record type is further divided into fields.

Each record type is detailed in this document. The description of each record type includes the following sections:

* Overview
* Record Format
* Details
* Verification/Validation/Value Authority Control
* Relationship to Other Record Types
* Example
* Known Problems

For records that are fully described in fixed column format, columns not assigned to fields must be left blank.

Types of Records

It is possible to group records into categories based upon how often the record type appears in an entry.

Single

There are records which may only appear one time (without continuations) in a file. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                
------------------------------------------------------------------------------
CRYST1            Unit cell parameters, space group, and Z.                   

END               Last record in the file.                                    

HEADER            First line of the entry, contains PDB ID code,              
                  classification, and date of deposition.                     

MASTER            Control record for bookkeeping.                             

ORIGXn            Transformation from orthogonal coordinates to the submitted 
                  coordinates (n = 1, 2, or 3).                               

SCALEn            Transformation from orthogonal coordinates to fractional    
                  crystallographic coordinates (n = 1, 2, or 3).              

It is an error for a duplicate of any of these records to appear in an entry.

Single Continued

There are records that conceptually exist only once in an entry, but the information content may exceed the number of columns available. These records are therefore continued on subsequent lines. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                  
-------------------------------------------------------------------------------
AUTHOR            List of contributors.                                        

CAVEAT            Severe error indicator.  Entries with this record must be    
                  used with care.                                              

COMPND            Description of macromolecular contents of the entry.         

EXPDTA            Experimental technique used for the structure determination. 

KEYWDS            List of keywords describing the macromolecule.               

OBSLTE            Statement that the entry has been removed from distribution  
                  and list of the ID code(s) which replaced it.                

SOURCE            Biological source of macromolecules in the entry.          

SPRSDE            List of entries withdrawn from release and replaced by       
                  current entry.                                               

TITLE             Description of the experiment represented in the entry.      

The second and subsequent lines contain a continuation field which is a right-justified integer. This number increments by one for each additional line of the record, and is followed by a blank character.

Multiple

Most record types appear multiple times, often in groups where the information is not logically concatenated but is presented in the form of a list. Many of these record types have a custom serialization that may be used not only to order the records, but also to connect to other record types. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                   
--------------------------------------------------------------------------------
ANISOU            Anisotropic temperature factors.                              

ATOM              Atomic coordinate records for standard groups.                

CISPEP            Identification of peptide residues in cis conformation.       

CONECT            Connectivity records.                                         

DBREF             Reference to the entry in the sequence database(s).           

HELIX             Identification of helical substructures.                      

HET               Identification of non-standard groups or residues (heterogens)

HETSYN            Synonymous compound names for heterogens.                     

HYDBND            Identification of hydrogen bonds.                             

LINK              Identification of inter-residue bonds.                        

MODRES            Identification of modifications to standard residues.         

MTRIXn            Transformations expressing non-crystallographic symmetry      
                  (n = 1, 2, or 3).  There may be multiple sets of these records.

REVDAT            Revision date and related information.                        

SEQADV            Identification of conflicts between PDB and the named sequence
                  database.                                                     

SEQRES            Primary sequence of backbone residues.                        

SHEET             Identification of sheet substructures.                        

SIGATM            Standard deviations of atomic parameters.                     

SIGUIJ            Standard deviations of anisotropic temperature factors.       

SITE              Identification of groups comprising important sites.          

SLTBRG            Identification of salt bridges                                

SSBOND            Identification of disulfide bonds.                            

TURN              Identification of turns.                                      

TVECT             Translation vector for infinite covalently connected          
                  structures.                                                   

Multiple Continued

There are records that conceptually exist multiple times in an entry, but the information content may exceed the number of columns available. These records are therefore continued on subsequent lines. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                  
-------------------------------------------------------------------------------
FORMUL            Chemical formula of non-standard groups.                      

HETATM            Atomic coordinate records for heterogens.                     

HETNAM            Compound name of the heterogens.                              

The second and subsequent lines contain a continuation field which is a right-justified integer. This number increments by one for each additional line of the record, and is followed by a blank character.

Grouping

There are three record types used to group other records. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                  
-------------------------------------------------------------------------------
ENDMDL            End-of-model record for multiple structures in a single      
                  coordinate entry.                                            

MODEL             Specification of model number for multiple structures in a   
                  single coordinate entry.                                     

TER               Chain terminator.                                            

The MODEL/ENDMDL records surround groups of ATOM, HETATM, SIGATM, ANISOU, SIGUIJ, and TER records. TER records indicate the end of a chain.

Other

The remaining record types have a detailed inner structure. Listed alphabetically, these are:

RECORD TYPE       DESCRIPTION                                                 
------------------------------------------------------------------------------
JRNL              Literature citation that defines the coordinate set.        

REMARK            General remarks, some are structured and some are free form.

Order of Records

All records in a PDB coordinate entry must appear in a defined order. Mandatory record types are present in all entries. When mandatory data are not provided, the record name must appear in the entry with a NULL indicator. Optional items become mandatory when certain conditions exist. Record order and existence are described in the following table:

RECORD TYPE             EXISTENCE      CONDITIONS IF OPTIONAL               
-------------------------------------------------------------------------------
HEADER                  Mandatory                                              

OBSLTE                  Optional       Mandatory in withdrawn entries.         

TITLE                   Mandatory                                              

CAVEAT                  Optional       Mandatory if structure is deemed        
                                       incorrect by an outside editorial board.

COMPND                  Mandatory                                              

SOURCE                  Mandatory                                              

KEYWDS                  Mandatory                                              

EXPDTA                  Mandatory                                              

AUTHOR                  Mandatory                                              

REVDAT                  Mandatory                                              

SPRSDE                  Optional       Mandatory if a replacement entry.      

JRNL                    Optional       Mandatory if a publication describes    
                                       the experiment.                         

REMARK 1                Optional                                               

REMARK 2                Mandatory                                              

REMARK 3                Mandatory                                              

REMARK N                Optional       Mandatory under certain conditions, as   
                                       noted in the remark descriptions.

DBREF                   Optional       Mandatory for each peptide chain with a 
                                       length greater than ten (10) residues, 
                                       and for nucleic acid entries that exist 
                                       in the Nucleic Acid Database (NDB).     

SEQADV                  Optional       Mandatory if sequence conflict exists.  

SEQRES                  Optional       Mandatory if ATOM records exist.      

MODRES                  Optional       Mandatory if modified group exists      
                                       within the coordinates.

HET                     Optional       Mandatory if non-standard group other  
                                       than water appears in the entry.       

HETNAM                  Optional       Mandatory if non-standard group other  
                                       than water appears in the entry.

HETSYN                  Optional                                     

FORMUL                  Optional       Mandatory if non-standard group or      
                                       water appears.                          

HELIX                   Optional                      

SHEET                   Optional                       

TURN                    Optional                         

SSBOND                  Optional       Mandatory if disulfide bond is present. 

LINK                    Optional                                               

HYDBND                  Optional                                               

SLTBRG                  Optional                                               

CISPEP                  Optional                                               

SITE                    Optional                                               

CRYST1                  Mandatory                                              

ORIGX1 ORIGX2 ORIGX3    Mandatory                                              

SCALE1 SCALE2 SCALE3    Mandatory                                              

MTRIX1 MTRIX2 MTRIX3    Optional       Mandatory if the complete asymmetric    
                                       unit must be generated from the given   
                                       coordinates using                       
                                       non-crystallographic symmetry.          

TVECT                   Optional                        

MODEL                   Optional       Mandatory if more than one model    
                                       is present in the entry.                

ATOM                    Optional       Mandatory if standard residues exist.   

SIGATM                  Optional                                               

ANISOU                  Optional                                               

SIGUIJ                  Optional                                               

TER                     Optional       Mandatory if ATOM records exist.        

HETATM                  Optional       Mandatory if non-standard group appears.

ENDMDL                  Optional       Mandatory if MODEL appears.             

CONECT                  Optional       Mandatory if non-standard group         
                                       appears.                                

MASTER                  Mandatory                                              

END                     Mandatory                                              

Note that a PDB file existing outside of the PDB official release may contain locally-defined records beginning with "USER". The PDB reserves the right to add new record types (not beginning with "USER"), so programs which read PDB entries should be prepared to read (and ignore) other record types. PDB will follow standard procedures whenever format changes are proposed.

Sections of an Entry

The following table lists the various sections of a PDB coordinate entry and the records comprising them:

SECTION              DESCRIPTION                    RECORD TYPE                 
--------------------------------------------------------------------------------
Title                Summary descriptive remarks    HEADER, OBSLTE, TITLE,       
                                                    CAVEAT, COMPND, SOURCE,      
                                                    KEYWDS, EXPDTA, AUTHOR,      
                                                    REVDAT, SPRSDE, JRNL         

Remark               Bibliography, refinement,      REMARKs 1, 2, 3 and others   
                     annotations                                           

Primary structure    Peptide and/or nucleotide      DBREF, SEQADV, SEQRES MODRES
                     sequence and the                                            
                     relationship between the PDB                                
                     sequence and that found in                                  
                     the sequence database(s)                                    

Heterogen            Description of non-standard    HET, HETNAM, HETSYN, FORMUL  
                     groups                                                      

Secondary structure  Description of secondary       HELIX, SHEET, TURN           
                     structure                                                   

Connectivity         Chemical connectivity          SSBOND, LINK, HYDBND,        
annotation                                          SLTBRG, CISPEP              

Miscellaneous        Features within the            SITE                   
  features           macromolecule                                               

Crystallographic     Description of the             CRYST1                       
                     crystallographic cell                                       

Coordinate           Coordinate transformation      ORIGXn, SCALEn, MTRIXn, TVECT
transformation       operators                                                   

Coordinate           Atomic coordinate data         MODEL, ATOM, SIGATM, ANISOU, 
                                                    SIGUIJ, TER, HETATM, ENDMDL  

Connectivity         Chemical connectivity          CONECT

Bookkeeping          Summary information,           MASTER, END                  
                     end-of-file marker                                          

The above information on Order of Records is repeated as Appendix 7.

Field Formats

Each record type is presented in a table which contains the division of the records into fields by column number, defined data type, field name or a quoted string which must appear in the field, and field definition. Any column not specified must be left blank.

Each field contains an identified data type which can be validated by a program. These are:

DATA TYPE          DESCRIPTION                                                    
----------------------------------------------------------------------------------
AChar              An alphabetic character (A-Z, a-z).    

Atom               Atom name which follow the naming rules in Appendix 3.         

Character          Any non-control character in the ASCII character set or a      
                   space.                                                         

Continuation       A two-character field that is either blank (for the first      
                   record of a set) or contains a two digit number                
                   right-justified and blank-filled which counts continuation     
                   records starting with 2.  The continuation number must be  
                   followed by a blank.                                        

Date               A 9 character string in the form dd-mmm-yy where DD is the     
                   day of the month, zero-filled on the left (e.g., 04); MMM is   
                   the common English 3-letter abbreviation of the month; and     
                   YY is a year in the 20th century.  This must represent a       
                   valid date.                                                    

IDcode             A PDB identification code which consists of 4 characters,      
                   the first of which is a digit in the range 0 - 9; the          
                   remaining 3 are alpha-numeric, and letters are upper case      
                   only.  Entries with a 0 as the first character do not          
                   contain coordinate data.                                       

Integer            Right-justified blank-filled integer value.                    

Token              A sequence of non-space characters followed by a colon and a   
                   space.                                                         

List               A String that is composed of text separated with commas.       

LString            A literal string of characters.  All spacing is significant    
                   and must be preserved.                                         

LString(n)         An LString with exactly n characters.                          

Real(n,m)          Real (floating point) number in the FORTRAN format Fn.m.       

Record name        The name of the record: 6 characters, left-justified and       
                   blank-filled.                                                  

Residue name       One of the standard amino acid or nucleic acids, as listed     
                   below, or the non-standard group designation as defined in     
                   the HET dictionary.  Field is right-justified.                  

SList              A String that is composed of text separated with semi-colons.  

Specification      A String composed of a token and its associated value          
                   separated by a colon.                                         

Specification      A sequence of Specifications, separated by semi-colons.        
  list                                                                            

String             A sequence of characters.  These characters may have           
                   arbitrary spacing, but should be interpreted as directed       
                   below.                                                         

String(n)          A String with exactly n characters.                            

SymOP              An integer field of from 4 to 6 digits, right-justified, of   
                   the form nnnMMM where nnn is the symmetry operator number and  
                   MMM is the translation vector.  See details in Appendix 1.

To interpret a String, concatenate the contents of all continued fields together, collapse all sequences of multiple blanks to a single blank, and remove any leading and trailing blanks. This permits very long strings to be properly reconstructed.

The above information about field formats is repeated as Appendix 6.

Residue Names

Standard residue names used in PDB entries:

RESIDUE TYPE       RESIDUE NAME                                                   
----------------------------------------------------------------------------------
Amino acids        ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS,    
                   MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX               

Nucleic acids      A, C, G, T, U, I, +A, +C, +G, +T, +U, +I                       

Other              UNK (unknown)                                                  

See Appendix 4 for more information on the standard residue names and abbreviations, and Appendix 5 for their chemical formulas and molecular weights.



2. Title Section

This section contains records used to describe the experiment and the biological macromolecules present in the entry: HEADER, OBSLTE, TITLE, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRNL, and REMARK records.


HEADER

Overview

The HEADER record uniquely identifies a PDB entry through the idCode field. This record also provides a classification for the entry. Finally, it contains the date the coordinates were deposited at the PDB.

Record Format

COLUMNS        DATA TYPE       FIELD           DEFINITION                           
----------------------------------------------------------------------------------
 1 -  6        Record name     "HEADER"                                             

11 - 50        String(40)      classification  Classifies the molecule(s)           

51 - 59        Date            depDate         Deposition date.  This is the date   
                                               the coordinates were received by     
                                               the PDB                              

63 - 66        IDcode          idCode          This identifier is unique within PDB 

Details

* The classification string is left-justified and exactly matches one of a collection of strings. See the class list available from the WWW site. In the case of macromolecular complexes, the classification field must present a class for each macromolecule present. Due to the limited length of the classification field, strings must sometimes be abbreviated. In these cases, the full terms are given in KEYWDS.

* Classification may be based on function, metabolic role, molecule type, cellular location, etc. In the case of a molecule having a dual function, both may be presented here. A list of valid terms that may be used as the classification appears on PDB's Web server (available at URL http://www.pdb.bnl.gov/Format.doc/Format_Home.html).

Verification/Validation/Value Authority Control

The verification program checks that the deposition date is a legitimate date and that the ID code is well-formed. PDB coordinate entry ID codes do not begin with 0, as this is used to identify the NOC files which are bibliographic only, not structural entries. The status and deposition date of an entry are checked against the PDB SYBASE tables, which provide a definitive list of existing ID codes.

Relationships to Other Record Types

The classification found in HEADER also appears in KEYWDS, unabbreviated and in no strict order.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
HEADER    MUSCLE PROTEIN                          02-JUN-93   1MYS

HEADER    HYDROLASE (CARBOXYLIC ESTER)            08-APR-93   2PHI

HEADER    COMPLEX (LECTIN/TRANSFERRIN)            07-JAN-94   1LGB


OBSLTE

Overview

OBSLTE appears in entries which have been withdrawn from distribution.

This record acts as a flag in an entry which has been withdrawn from the PDB's full release. It indicates which, if any, new entries have replaced the withdrawn entry.

The format allows for the case of multiple new entries replacing one existing entry.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                          
----------------------------------------------------------------------------------
 1 -  6        Record name     "OBSLTE"                                           

 9 - 10        Continuation    continuation   Allows concatenation of multiple    
                                              records.                         

12 - 20        Date            repDate        Date that this entry was replaced.  

22 - 25        IDcode          idCode         ID code of this entry.              

32 - 35        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

37 - 40        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

42 - 45        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

47 - 50        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

52 - 55        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

57 - 60        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

62 - 65        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

67 - 70        IDcode          rIdCode        ID code of entry that replaced      
                                              this one.                           

Details

* It is PDB policy that only the primary author who submitted an entry has the authority to withdraw it. All withdrawn entries are available for research purposes. PDB should be contacted in cases where the withdrawn data are desired.

Verification/Validation/Value Authority Control

PDB staff add this record at the time an entry is removed from release.

Relationships to Other Record Types

None.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
OBSLTE     31-JAN-94 1MBP      2MBP


TITLE

Overview

The TITLE record contains a title for the experiment or analysis that is represented in the entry. It should identify an entry in the PDB in the same way that a title identifies a paper.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                            
----------------------------------------------------------------------------------
 1 -  6        Record name     "TITLE "                                             

 9 - 10        Continuation    continuation   Allows concatenation of multiple      
                                              records.                              

11 - 70        String          title          Title of the experiment.              

Details

* The title of the entry is free text and should describe the contents of the entry and any procedures or conditions that distinguish this entry from similar entries. It presents an opportunity for the depositor to emphasize the underlying purpose of this particular experiment.

* Some items that may be included in TITLE are:

- Experiment type.
- Description of the mutation.
- The fact that only alpha carbon coordinates have been provided in the entry.

Verification/Validation/Value Authority Control

This record is free text so no verification of format is required. The title is supplied by the depositor, but PDB staff may exercise editorial judgment in consultation with depositors in assigning the title.

Relationships to Other Record Types

COMPND, SOURCE, EXPDTA, and REMARKs provide information that may also be found in TITLE. You may think of the title as describing the experiment, and the compound record as describing the molecule(s).

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
TITLE     RHIZOPUSPEPSIN COMPLEXED WITH REDUCED PEPTIDE INHIBITOR

TITLE     BETA-GLUCOSYLTRANSFERASE, ALPHA CARBON COORDINATES ONLY

TITLE     NMR STUDY OF OXIDIZED THIOREDOXIN MUTANT (C62A,C69A,C73A)
TITLE    2 MINIMIZED AVERAGE STRUCTURE


CAVEAT

Overview

CAVEAT warns of severe errors in an entry. Use caution when using an entry containing this record.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                          
----------------------------------------------------------------------------------
 1 -  6        Record name     "CAVEAT"                                           

 9 - 10        Continuation    continuation   Allows concatenation of multiple    
                                              records.                            

12 - 15        IDcode          idCode         PDB ID code of this entry.          

20 - 70        String          comment        Free text giving the reason for the 
                                              CAVEAT.                             

Details

* PDB will add this record to incorrect entries that are not withdrawn from the set of released entries. This record will be used sparingly, and only after an external review has been made.

* Please note the CAVEAT will also be included in cases where PDB is unable to verify the transformation back to the crystallographic cell. In these cases, the molecular structure may still be correct.

Verification/Validation/Value Authority Control

CAVEAT will be added by the PDB to entries known to be incorrect.

Relationships to Other Record Types

REMARK 5 repeats the comment field of the CAVEAT record.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
CAVEAT     1ABC    THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS
CAVEAT   2 1ABC    UNCORRECTABLE AT THIS TIME


COMPND

Overview

The COMPND record describes the macromolecular contents of an entry. Each macromolecule found in the entry is described by a set of token: value pairs, and is referred to as a COMPND record component. Since the concept of a molecule is difficult to specify exactly, PDB staff may exercise editorial judgment in consultation with depositors in assigning these names.

For each macromolecular component, the molecule name, synonyms, number assigned by the Enzyme Commission (EC), and other relevant details are specified.

Record Format

COLUMNS        DATA TYPE         FIELD          DEFINITION                        
----------------------------------------------------------------------------------
 1 -  6        Record name       "COMPND"                                         

 9 - 10        Continuation      continuation   Allows concatenation of multiple  
                                                records.                          

11 - 70        Specification     compound       Description of the molecular      
               list                             components.                  

Details

* The compound record is a Specification list. The specifications, or tokens, that may be used are listed below:

TOKEN                   VALUE DEFINITION                                       
---------------------------------------------------------------------------------
MOL_ID                  Numbers each component; also used in SOURCE to associate 
                        the information.   

MOLECULE                Name of the macromolecule.         

CHAIN                   Comma-separated list of chain identifier(s). "NULL" is   
                        used to indicate a blank chain identifier.     

FRAGMENT                Specifies a domain or region of the molecule.            

SYNONYM                 Comma-separated list of synonyms for the MOLECULE.       

EC                      The Enzyme Commission number associated with the         
                        molecule. If there is more than one EC number, they     
                        are presented as a comma-separated list.                 

ENGINEERED              Indicates that the molecule was produced using           
                        recombinant technology or by purely chemical synthesis.  

MUTATION                Describes mutations from the wild type molecule.         

BIOLOGICAL_UNIT         If the MOLECULE functions as part of a larger            
                        biological unit, the entire functional unit may be       
                        described.                                               

OTHER_DETAILS           Additional comments.                                     

* In the general case the PDB tends to reflect the biological/functional view of the molecule. For example, the hetero-tetramer hemoglobin molecule is treated as a discrete component in COMPND.

* In the case of synthetic molecules, e. g., hybrids, the description will be provided by the depositor.

* No specific rules apply to the ordering of the tokens, except that the occurrence of MOL_ID or FRAGMENT indicates that the subsequent tokens are related to that specific molecule or fragment of the molecule.

* Physical layout of these items may be altered by PDB staff to improve human readability of the COMPND record.

* Asterisks in nucleic acid names (in MOLECULE) are for ease of reading.

* When insertion codes are given as part of the residue name, they must be given within square brackets, i.e., H57[A]N. This might occur when listing residues in FRAGMENT, MUTATION, or OTHER_DETAILS.

* For multi-chain molecules, e.g., the hemoglobin tetramer, a comma-separated list of CHAIN identifiers is used.

* When non-blank chain identifiers occur in the entry, they must be specified.

* NULL is used to indicate blank chain identifiers. E.g., CHAIN: NULL, CHAIN: NULL, B, C.

* For enzymes, if no EC number has been assigned, "EC: NOT ASSIGNED" is used.

* ENGINEERED is followed either by "YES" or by a comment.

* For the token MUTATION, the following set of examples illustrate the conventions used by PDB to represent various types of mutations.

   MUTATION TYPE         DESCRIPTION                     FORM   
   ------------------------------------------------------------------------------
   Simple substitution   His 57 replaced by Asn          H57N 

                         His 57A replaced by Asn, in       
                         chain C only                    Chain C, H57[A]N

   Insertion             His and Pro inserted before      
                         Lys 48                          INS(HP-K48) 

   Deletion              Arg 141 of chains A and C        
                         deleted, not deleted in           
                         chain B                         Chain A, C, DEL(R141)

                         His 23 through ARG 26 deleted   DEL(23-26)

                         His 23C and Arg 26 deleted       
                         from chain B only               Chain B, DEL(H23[C],R26)

* When there are more than ten mutations:

- All the mutations are listed in the SEQADV record.
- Some mutations may be listed in MUTATION in COMPND to highlight the most important ones, at the depositor's discretion.

* New tokens may be added by the PDB as needed.

Verification/Validation/Value Authority Control

CHAIN must match the chain identifiers(s) of the molecule(s). EC numbers are checked against the Enzyme Data Bank.

Relationships to Other Record Types

Each molecule given a MOL_ID in COMPND must be listed and given the biological source information in SOURCE. In the case of mutations, the SEQADV records will present differences from the reference molecule. REMARK record may further describe the contents of the entry. Also see verification above.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
COMPND    MOL_ID: 1;                                                  
COMPND   2 MOLECULE: HEMOGLOBIN;                                      
COMPND   3 CHAIN: A, B, C, D;                                         
COMPND   4 ENGINEERED: YES;                                           
COMPND   5 MUTATION: CHAIN B, D, V1A;                                 
COMPND   6 BIOLOGICAL_UNIT: HEMOGLOBIN EXISTS AS AN A1B1/A2B2         
COMPND   7 TETRAMER;
COMPND   8 OTHER_DETAILS: DEOXY FORM  

COMPND    MOL_ID: 1;                                            
COMPND   2 MOLECULE: COWPEA CHLOROTIC MOTTLE VIRUS;             
COMPND   3 CHAIN: A, B, C;                                      
COMPND   4 SYNONYM: CCMV;                                       
COMPND   5 MOL_ID: 2;                                           
COMPND   6 MOLECULE: RNA (5'-(*AP*UP*AP*U)-3');               
COMPND   7 CHAIN: D, F;
COMPND   8 ENGINEERED: YES;                                     
COMPND   9 MOL_ID: 3;                                           
COMPND  10 MOLECULE: RNA (5'-(*AP*U)-3');                      
COMPND  11 CHAIN: E;
COMPND  12 ENGINEERED: YES

COMPND    MOL_ID: 1;                                            
COMPND   2 MOLECULE: HEVAMINE A;                                
COMPND   3 CHAIN: NULL;                                         
COMPND   4 EC: 3.2.1.14, 3.2.1.17;                              
COMPND   5 OTHER_DETAILS: PLANT ENDOCHITINASE/LYSOZYME          


SOURCE

Overview

The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied.

Record Format

COLUMNS        DATA TYPE         FIELD          DEFINITION                        
----------------------------------------------------------------------------------
 1 -  6        Record name       "SOURCE"                                         

 9 - 10        Continuation      continuation   Allows concatenation of multiple  
                                                records.                         

11 - 70        Specification     srcName        Identifies the source of the      
               list                             macromolecule in a token: value 
                                                format.                        

Details

TOKEN                                VALUE DEFINITION                        
---------------------------------------------------------------------------------
MOL_ID                               Numbers each molecule.  Same as appears in  
                                     COMPND.                                     

SYNTHETIC                            Indicates a chemically-synthesized source.  

FRAGMENT                             A domain or fragment of the molecule may be 
                                     specified.                                  

ORGANISM_SCIENTIFIC                  Scientific name of the organism.            

ORGANISM_COMMON                      Common name of the organism.                

STRAIN                               Identifies the strain.                      

VARIANT                              Identifies the variant.                     

CELL_LINE                            The specific line of cells used in the      
                                     experiment.                                 

ATCC                                 American Type Culture Collection tissue     
                                     culture number.                             

ORGAN                                Organized group of tissues that carries on  
                                     a specialized function.                     

TISSUE                               Organized group of cells with a common     
                                     function and structure.                     

CELL                                 Identifies the particular cell type.        

ORGANELLE                            Organized structure within a cell.          

SECRETION                            Identifies the secretion, such as saliva, 
                                     urine, or venom, from which the molecule was
                                     isolated. 

CELLULAR_LOCATION                    Identifies the location inside (or
                                     outside) the cell.

PLASMID                              Identifies the plasmid containing the gene. 

GENE                                 Identifies the gene.                        

EXPRESSION_SYSTEM                    System used to express recombinant         
                                     macromolecules.                             

EXPRESSION_SYSTEM_STRAIN             Strain of the organism in which the molecule
                                     was expressed.                              

EXPRESSION_SYSTEM_VARIANT            Variant of the organism used as the 
                                     expression system.

EXPRESSION_SYSTEM_CELL_LINE          The specific line of cells used as the 
                                     expression system.

EXPRESSION_SYSTEM_ATCC_NUMBER        Identifies the ATCC number of the expression
                                     system

EXPRESSION_SYSTEM_ORGAN              Specific organ which expressed the molecule.

EXPRESSION_SYSTEM_TISSUE             Specific tissue which expressed the molecule.

EXPRESSION_SYSTEM_CELL               Specific cell type which expressed the 
                                     molecule.

EXPRESSION_SYSTEM_ORGANELLE          Specific organelle which expressed the 
                                     molecule.

EXPRESSION_SYSTEM_CELLULAR_LOCATION  Identifies the location inside or outside 
                                     the cell which expressed the molecule.

EXPRESSION_SYSTEM_VECTOR_TYPE        Identifies the type of vector used, i.e., 
                                     plasmid, virus, or cosmid.

EXPRESSION_SYSTEM_VECTOR             Identifies the vector used.

EXPRESSION_SYSTEM_PLASMID            Plasmid used in the recombinant experiment. 

EXPRESSION_SYSTEM_GENE               Name of the gene used in recombinant       
                                     experiment.                                

OTHER_DETAILS                        Used to present information on the source 
                                     which is not given elsewhere.              

* The srcName is a list of token: value pairs describing each biological component of the entry.

* As in COMPND, the order is not specified except that MOL_ID or FRAGMENT indicates subsequent specifications are related to that molecule or fragment of the molecule.

* Physical layout of these items may be altered by PDB staff to improve human readability of the SOURCE record.

* Only the relevant tokens need to appear in an entry.

* Molecules prepared by purely chemical synthetic methods are described by the specification SYNTHETIC followed by "YES" or an optional value, such as NON-BIOLOGICAL SOURCE or BASED ON THE NATURAL SEQUENCE. ENGINEERED must appear in the COMPND record.

* In the case of a chemically synthesized molecule using a biologically functional sequence (nucleic or amino acid), SOURCE reflects the biological origin of the sequence and COMPND reflects its synthetic nature by inclusion of the token ENGINEERED. The token SYNTHETIC appears in SOURCE.

* If made from a synthetic gene, ENGINEERED appears in COMPND and the expression system is described in SOURCE (SYNTHETIC does NOT appear in SOURCE).

* If the molecule was made using recombinant techniques, ENGINEERED appears in COMPND and the system is described in SOURCE.

* When multiple macromolecules appear in the entry, each MOL_ID, as given in the COMPND record, must be repeated in the SOURCE record along with the source information for the corresponding molecule.

* Hybrid molecules prepared by fusion of genes are treated as multi-molecular systems for the purpose of specifying the source. The token FRAGMENT is used to associate the source with its corresponding fragment.

- When necessary to fully describe hybrid molecules, tokens may appear more than once for a given MOL_ID.
- All relevant token: value pairs that taken together fully describe each fragment are grouped following the appropriate FRAGMENT.
- Descriptors relative to the full system appear before the FRAGMENT (see Example 3 below).

* ORGANISM_SCIENTIFIC provides the Latin genus and species. Virus names are listed as the scientific name.

* Cellular origin is described by giving cellular compartment, organelle, cell, tissue, organ, or body part from which the molecule was isolated.

* CELLULAR_LOCATION may be used to indicate where in the organism the compound was found. Examples are: extracellular, periplasmic, cytosol.

* Entries containing molecules prepared by recombinant techniques are described as follows:

- The expression system is described.
- The organism and cell location given are for the source of the gene used in the cloning experiment.
- Transgenic organisms, such as mouse producing human proteins, are treated as expression systems.

* For a theoretical modelling experiment, SOURCE describes the modelled compound just as though it were an experimental study.

* New tokens may be added by the PDB.

Verification/Validation/Value Authority Control

The biological source is compared to that found in the sequence database. Common and scientific names are checked against the "Annotated Classification of Source Organisms: PIR-International Protein Sequence Database" compiled by Andrzej Elzanowski and available from the PDB.

Relationships to Other Record Types

Each macromolecule listed in COMPND must have a corresponding source.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SOURCE    MOL_ID: 1;                                   
SOURCE   2 ORGANISM_SCIENTIFIC: AVIAN SARCOMA VIRUS;   
SOURCE   3 STRAIN: SCHMIDT-RUPPIN B;                   
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;        
SOURCE   5 EXPRESSION_SYSTEM_PLASMID: PRC23IN

SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
SOURCE   3 ORGANISM_COMMON: CHICKEN;
SOURCE   4 ORGAN: HEART;
SOURCE   5 TISSUE: MUSCLE

SOURCE    MOL_ID: 1;
SOURCE   2 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   3 EXPRESSION_SYSTEM_STRAIN: BE167;
SOURCE   4 FRAGMENT: RESIDUES 1-16;
SOURCE   5 ORGANISM_SCIENTIFIC: BACILLUS AMYLOLIQUEFACIENS;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 FRAGMENT: RESIDUES 17-214;
SOURCE   8 ORGANISM_SCIENTIFIC: BACILLUS MACERANS


KEYWDS

Overview

The KEYWDS record contains a set of terms relevant to the entry. Terms in the KEYWDS record provide a simple means of categorizing entries and may be used to generate index files. This record addresses some of the limitations found in the classification field of the HEADER record. It provides the opportunity to add further annotation to the entry in a concise and computer-searchable fashion.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
---------------------------------------------------------------------------------
 1 -  6        Record name     "KEYWDS"                                          

 9 - 10        Continuation    continuation   Allows concatenation of records if 
                                              necessary.                         

11 - 70        List            keywds         Comma-separated list of keywords   
                                              relevant to the entry.            

Details

* The KEYWDS record contains a list of terms relevant to the entry, similar to that found in journal articles. A phrase may be used if it presents a single concept (e.g., reaction center). Terms provided in this record may include those that describe the following:

- Functional classification.
- Metabolic role.
- Known biological or chemical activity.
- Structural classification.

*Other classifying terms may be used. No ordering is required for these terms. A number of PDB entries contain complexes of macromolecules. In these cases, all terms applicable to each molecule should be provided.

*Note that the terms in the KEYWDS record duplicate those found in the classification field of the HEADER record. Terms abbreviated in the HEADER record are unabbreviated in KEYWDS, and the parentheses used in HEADER are optional in KEYWDS.

Verification/Validation/Value Authority Control

Terms used in the KEYWDS record are subject to scientific and editorial review. A list of terms, definitions, and synonyms will be maintained at the PDB. Every attempt will be made to provide some level of consistency with keywords used in other biological databases.

Relationships to Other Record Types

HEADER records contain a classification term which must also appear in KEYWDS. Scientific judgment will dictate when terms used in one entry to describe a molecule should be included in other entries with the same or similar molecules.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
KEYWDS    LYASE, TRICARBOXYLIC ACID CYCLE, MITOCHONDRION, OXIDATIVE
KEYWDS   2 METABOLISM


EXPDTA

Overview

The EXPDTA record presents information about the experiment.

The EXPDTA record identifies the experimental technique used. This may refer to the type of radiation and sample, or include the spectroscopic or modeling technique. Permitted values include:

ELECTRON DIFFRACTION
FIBER DIFFRACTION
FLUORESCENCE TRANSFER
NEUTRON DIFFRACTION
NMR
THEORETICAL MODEL
X-RAY DIFFRACTION

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                          
-------------------------------------------------------------------------------
 1 -  6       Record name    "EXPDTA"                                          

 9 - 10       Continuation   continuation  Allows concatenation of multiple    
                                           records.                            

11 - 70       SList          technique     The experimental technique(s) with  
                                           optional comment describing the     
                                           sample or experiment. 

Details

* EXPDTA is mandatory and appears in all entries.

* The technique must match one of the permitted values. See above.

* If more than one model appears in the entry, the number of models included must be stated.

* If only one model appears in the entry, its significance must be stated, such as it being a minimized average or regularized mean structure.

* If more than one technique was used for the structure determination and is being represented in the entry, EXPDTA presents the techniques as a semi-colon separated list. Each technique may have a comment, which appears before the semi-colon.

Verification/Validation/Value Authority Control

The verification program checks that the EXPDTA record appears in the entry and that the technique matches one of the allowed values. It also checks that the relevant standard REMARK is added in the case of NMR, fiber, or theoretical modeling studies, and that the correct CRYST1 and SCALE are used in these cases. If an entry contains multiple models, the verification program checks for the correct number of matching MODEL/ENDMDL records.

Relationships to Other Record Types

If the experiment is an NMR, fiber, or theoretical modeling study, this may be stated in the TITLE, and the appropriate EXPDTA and REMARK records should appear. Specific details of the data collection and experiment appear in the REMARKs.

In the case of a polycrystalline fiber diffraction study, CRYST1 and SCALE contain the normal unit cell data.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
EXPDTA    X-RAY DIFFRACTION

EXPDTA    NEUTRON DIFFRACTION; X-RAY DIFFRACTION

EXPDTA    NMR, 32 STRUCTURES

EXPDTA    NMR, REGULARIZED MEAN STRUCTURE

EXPDTA    THEORETICAL MODEL

EXPDTA    FIBER DIFFRACTION, FIBER

EXPDTA    FIBER DIFFRACTION, POLYCRYSTALLINE SAMPLE


AUTHOR

Overview

The AUTHOR record contains the names of the people responsible for the contents of the entry.

Record Format

 
COLUMNS       DATA TYPE      FIELD         DEFINITION                             
----------------------------------------------------------------------------------
 1 -  6       Record name    "AUTHOR"                                             

 9 - 10       Continuation   continuation  Allows concatenation of multiple       
                                           records.                               

11 - 70       List           authorList    List of the author names, separated    
                                           by commas.                             

Details

* The authorList field lists author names separated by commas with no subsequent spaces.

* Representation of personal names:

- First and middle names are indicated by initials, each followed by a period, and precede the surname.
- Only the surname (family or last name) of the author is given in full.
- Hyphens can be used if they are part of the author's name.
- Apostrophes are allowed in surnames.
- The word Junior is not abbreviated.
- Umlauts and other character modifiers are not given.

* Structure of personal names:

- There is no space after any initial and its following period.
- Blank spaces are used in a name only if properly part of the surname (e.g., J.VAN DORN), or between surname and Junior, II, or III.
- Abbreviations that are part of a surname, such as St. or Ste., are followed by a period and a space before the next part of the surname.

* Representation of corporate names:

- Group names used for one or all of the authors should be spelled out in full.
- The name of the larger group comes before the name of a subdivision, e.g., University of Somewhere Department of Chemistry.

* Structure of list:

- Line breaks between multiple lines in the authorList occur only after a comma.
- Personal names are not split across two lines.

* Special cases:

- Names are given in English if there is an accepted English version; otherwise in the native language, transliterated if necessary.
- "ET AL." may be used when all authors are not individually listed.

Verification/Validation/Value Authority Control

The verification program checks that the authorList field is correctly formatted. It does not perform any spelling checks or name verification.

Relationships to Other Record Types

The format of the names in the AUTHOR record is the same as in JRNL and REMARK 1 references.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
AUTHOR    M.B.BERRY,B.MEADOR,T.BILDERBACK,P.LIANG,M.GLASER,
AUTHOR   2 G.N.PHILLIPS JUNIOR,T.L.ST. STEVENS

AUTHOR    C.-I.BRANDEN,C.J.BIRKETT-CLEWS,L.RIVA DI SANSAVERINO


REVDAT

Overview

REVDAT records contain a history of the modifications made to an entry since its release.

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                             
----------------------------------------------------------------------------------
 1 -  6       Record name    "REVDAT"                                             

 8 - 10       Integer        modNum        Modification number.                   

11 - 12       Continuation   continuation  Allows concatenation of multiple      
                                           records.                         

14 - 22       Date           modDate       Date of modification (or release for   
                                           new entries).  This is not repeated    
                                           on continuation lines.                 

24 - 28       String(5)      modId         Identifies this particular             
                                           modification.  It links to the         
                                           archive used internally by PDB.        
                                           This is not repeated on continuation   
                                           lines.                                 

32            Integer        modType       An integer identifying the type of     
                                           modification.  In case of revisions    
                                           with more than one possible modType,   
                                           the highest value applicable will be   
                                           assigned.                              

40 - 45       LString(6)     record        Name of the modified record.           

47 - 52       LString(6)     record        Name of the modified record.           

54 - 59       LString(6)     record        Name of the modified record.           

61 - 66       LString(6)     record        Name of the modified record.           

Details

* Each time revisions are made to the entry, a modification number is assigned in increasing (by 1) numerical order. REVDAT records appear in descending order (most recent modification appears first). New entries have a REVDAT record with modNum equal to 1 and modType equal to 0. Allowed modTypes are:

         0       Initial released entry. 
         1       Miscellaneous - mostly typographical.   
         2       Modification of a CONECT record.        
         3       Modification to coordinates or transformations. 
         4 - 9   Not defined.

* Each revision may have more than one REVDAT record, and each revision has a separate continuation field.

Verification/Validation/Value Authority Control

The modType must be one of the defined types, and the given record type must be valid. If modType is 0, the modId must match the entry's ID code in the HEADER record.

Relationships to Other Record Types

REMARK 860 presents the correction or change that is made to an entry. Also, see verification above.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REVDAT   3   15-OCT-89 1PRCB   1       REMARK                         
REVDAT   2   19-APR-89 1PRCA   2       CONECT                         
REVDAT   1   09-JAN-89 1PRC    0                                      


SPRSDE

Overview

The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set. One entry may replace many. It is PDB policy that only the principal investigator of a structure has the authority to withdraw it.

Record Format

COLUMNS       DATA TYPE      FIELD         DEFINITION                             
----------------------------------------------------------------------------------
 1 -  6       Record name    "SPRSDE"                                             

 9 - 10       Continuation   continuation  Allows for multiple ID codes.          

12 - 20       Date           sprsdeDate    Date this entry superseded the         
                                           listed entries. This field is not      
                                           copied on continuations.               

22 - 25       IDcode         idCode        ID code of this entry.  This field     
                                           is not copied on continuations.        

32 - 35       IDcode         sIdCode       ID code of a superseded entry.         

37 - 40       IDcode         sIdCode       ID code of a superseded entry.         

42 - 45       IDcode         sIdCode       ID code of a superseded entry.         

47 - 50       IDcode         sIdCode       ID code of a superseded entry.         

52 - 55       IDcode         sIdCode       ID code of a superseded entry.         

57 - 60       IDcode         sIdCode       ID code of a superseded entry.         

62 - 65       IDcode         sIdCode       ID code of a superseded entry.         

67 - 70       IDcode         sIdCode       ID code of a superseded entry.         

Details

* The ID code list is terminated by the first blank sIDcode field.

Verification/Validation/Value Authority Control

PDB checks that the superseded entries have actually been withdrawn from release.

Relationships to Other Record Types

The sprsdeDate is usually the date the entry is released, and therefore matches the date in the REVDAT 1 record. The ID code found in the idCode field must be the same as one found in the idCode field of the HEADER record.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SPRSDE     17-JUL-84 4HHB      1HHB

SPRSDE     27-FEB-95 1GDJ      1LH4 2LH4


JRNL

Overview

The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set. There is at most one JRNL reference per entry. If there is no primary reference, then there is no JRNL reference. Other references are given in REMARK 1.

PDB is in the process of linking and/or adding all references to CitDB, the literature database used by the Genome Data Base (available at URL http://gdbwww.gdb.org/gdb-bin/genera/genera/citation/Citation).

Record Format

COLUMNS    DATA TYPE      FIELD     DEFINITION                                   
----------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                               

13 - 70    LString        text      See Details below.                            

Details

* The following tables are used to describe the sub-record types of the JRNL record.

* The AUTH sub-record is mandatory in JRNL. This is followed by TITL, EDIT, REF, PUBL, and REFN sub-record types. REF and REFN are also mandatory in JRNL. EDIT and PUBL may appear only if the reference is to a non-journal.

* If the JRNL reference is in the MEDLINE database the information in the MEDLINE reference will be used to supply information for the sub-record types.

* When a MEDLINE reference is used, the abbreviation of the journal will be converted to the CASSI abbreviation as listed in the coden list used jointly by the Cambridge Crystallographic Data Centre (CCDC) and the PDB.

1. AUTH

* AUTH contains the list of authors associated with the cited article or contribution to a larger work (i.e., AUTH is not used for the editor of a book).

* The author list is formatted similarly to the AUTHOR record. It is a comma-separated list of names. Spaces at the end of a sub-record are not significant; all other spaces are significant. See the AUTHOR record for full details.

* The authorList field of continuation sub-records in JRNL differs from that in AUTHOR by leaving no leading blank in column 20 of any continuation lines.

* One author's name, consisting of the initials and family name, cannot be split across two lines. If there are continuation sub-records, then all but the last sub-record must end in a comma.

COLUMNS    DATA TYPE      FIELD         DEFINITION                               
-------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                               

13 - 16    LString(4)     "AUTH"        Appears on all continuation records.     

17 - 18    Continuation   continuation  Allows concatenation of multiple         
                                        records.                                 

20 - 70    List           authorList    List of the authors.                     

2. TITL

* TITL specifies the title of the reference. This is used for the title of a journal article, chapter, or part of a book. The TITL line is omitted if the author(s) listed in authorList wrote the entire book (or other work) listed in REF and no section of the book is being cited.

* If an article is in a language other than English and is printed with an alternate title in English, the English language title is given, followed by a space and then the name of the language (in its English form, in square brackets) in which the article is written.

* If the title of an article is in a non-Roman alphabet the title is transliterated.

* The actual title cited is reconstructed in a manner identical to other continued records, i.e., trailing blanks are discarded and the continuation line is concatenated with a space inserted.

* A line cannot end with a hyphen. A compound term (two elements connected by a hyphen) or chemical names which include a hyphen must appear on a single line, unless they are too long to fit on one line, in which case the split is made at a normally-occurring hyphen. An individual word cannot be hyphenated at the end of a line and put on two lines. An exception is when there is a repeating compound term where the second element is omitted, e.g., "DOUBLE- AND TRIPLE-RESONANCE". In such a case the non-completed word "DOUBLE-" could end a line and not alter reconstruction of the title.

COLUMNS    DATA TYPE      FIELD         DEFINITION                               
-------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                               

13 - 16    LString(4)     "TITL"        Appears on all continuation lines.        

17 - 18    Continuation   continuation  Permits long titles.                      

20 - 70    LString        title         Title of the article.                     

3. EDIT

* EDIT appears if editors are associated with a non-journal reference. The editor list is formatted and concatenated in the same way that author lists are.

COLUMNS    DATA TYPE      FIELD         DEFINITION                               
-------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                               

13 - 16    LString(4)     "EDIT"        Appears on all continuation records.      

17 - 18    Continuation   continuation  Allows a long list of editors.            

20 - 70    List           editorList    List of the editors.                      

4. REF

* REF is a group of fields which contains either the publication status or the name of the publication (and any supplement and/or report information), volume, page, and year. There are two forms of this sub-record group, depending upon the citation's publication status.

4a. If the reference has not yet been published, the sub-record type group has the form:

COLUMNS    DATA TYPE      FIELD                   DEFINITION                      
--------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                                

13 - 16    LString(3)     "REF"                                                   

20 - 34    LString(15)    "TO BE PUBLISHED"                                       

* At the present time, there is no formal mechanism in place for monitoring the subsequent publication of such referenced papers. PDB relies upon the depositor to provide reference update information since preliminary information can change by the time of actual publication.

4b. If the reference has been published, then the REF sub-record type contains information about the name of the publication, supplement, report, volume, page, and year in the appropriate fields. These fields are detailed below.

* Publication name (first item in pubName field):

- If the publication is a serial (i.e., a journal, an annual, or other non-book or non-monographic item issued in parts and intended to be continued indefinitely), use the abbreviated name of the publication as listed in American Chemical Society (A.C.S.) publications such as CAS Source Index (CASSI) or Chemical Abstracts. (The A.C.S. abbreviation is based on the International Standards Organization's standard ISO 4-1984[E].) If the A.C.S. has not yet established an abbreviation for the publication, the name is given in full.
- If the publication is a book, monograph, or other non-serial item, use its full name according to the Anglo-American Cataloging Rules, 2nd Ed., 1988 revision (AACR2R). (Non-serial items include theses, videos, computer programs, and anything that is complete in one or a finite number of parts.) If there is a sub-title, and the item is verified in an online catalog, it will be included using the same punctuation as in the source of verification. Preference will be given to verification using cataloging of the Library of Congress, the National Library of Medicine, and the British Library, in that order.
- If a book is part of a monographic series: the full name of the book (according to AACR2R) is listed first, followed by the name of the series in which it was published. The series information is given within parentheses and the series name is preceded by "IN:" and a space. If the series has an A.C.S. abbreviation, that abbreviation should be used; otherwise the series name should be listed in full. If applicable, the series name should be followed, after a comma and a space, by a volume (V.) and/or number (NO.) and/or part (PT.) indicator and the relevant characters to indicate its number and/or letter in the series.

* Supplement (follows publication name in pubName field):

- If a reference is in a supplement to the volume listed, or if information about a "part" is needed to distinguish multiple parts with the same page numbering, such information should be put in the REF sub-record.
- A supplement indication should follow the name of the publication and should be preceded by a comma and a space. Supplement should be abbreviated as "SUPPL." If there is a supplement number or letter, it should follow "SUPPL." without an intervening space. A part indication should also follow the name of the publication and be preceded by a comma and a space. A part should be abbreviated as "PT.", and the number or letter should follow without an intervening space.
- If there is both a supplement and a part, their order should reflect the order printed on the work itself.

* Report (follows publication name and any supplement or part information in pubName field):

- If a book has a report designation, the report information should follow the title and precede series information. The name and number of the report is given in parentheses, and the name is preceded by "REPORT:" and a space.

* Reconstruction of publication name:

- The name of the publication is reconstructed by removing any trailing blanks in the pubName field, and concatenating all of the pubName fields from the continuation lines with an intervening space. There are two conditions where no intervening space is added between lines: when the pubName field on a line ends with a hyphen or a period, or when the line ends with a hyphen (-). When the line ends with a period (.), add a space if this is the only period in the entire pubName field; do not add a space if there are two or more periods throughout the pubName field, excluding any periods after the designations "SUPPL", "V", "NO", or "PT".

* Volume, page, and year (volume, page, year fields respectively):

- The REF sub-record type group also contains information about volume, page, and year when applicable.
- In the case of a monograph with multiple volumes which is also in a numbered series, the number in the volume field represents the volume number of the book, not the series. (The volume number of the series is in parentheses with the name of the series, as described above under publication name.)
COLUMNS    DATA TYPE     FIELD         DEFINITION                                
--------------------------------------------------------------------------------
 1 -  6    Record name   "JRNL  "                                                

13 - 16    LString(3)    "REF"                                                   

17 - 18    Continuation  continuation  Allows long publication names.            

20 - 47    LString       pubName       Name of the publication including         
                                       section or series designation.  This is   
                                       the only field of this sub-record which   
                                       may be continued on successive            
                                       sub-records.                              

50 - 51    LString(2)    "V."          Appears in the first sub-record only,     
                                       and only if column 55 is non-blank.       

52 - 55    String        volume        Right-justified blank-filled volume       
                                       information; appears in the first         
                                       sub-record only.                          

57 - 61    String        page          First page of the article; appears in the 
                                       first sub-record only.                    

63 - 66    Integer       year          Year of publication; first sub-record     
                                       only.                                      

5. PUBL

* PUBL contains the name of the publisher and place of publication if the reference is to a book or other non-journal publication. If the non-journal has not yet been published or released, this sub-record is absent.

* The place of publication is listed first, followed by a space, a colon, another space, and then the name of the publisher/issuer. This arrangement is based on the ISBD(M) International Standard Bibliographic Description for Monographic Publications (Rev.Ed., 1987) and AACR2R and is used in public online catalogs in libraries. Details on the contents of PUBL are given below.

* Place of publication:

- Give the place of publication. If the name of the country, state, province, etc. is considered necessary to distinguish the place of publication from others of the same name, or for identification, then follow the city with a comma, a space, and the name of the larger geographic area.
- If there is more than one place of publication, only the first listed will be used. If an online catalog record is used to verify the item, the first place listed there will be used, omitting any brackets. Preference will be given to the cataloging done by the Library of Congress, the National Library of Medicine, and the British Library, in that order.

* Publisher's name (or name of other issuing entity):

- Give the name of the publisher in the shortest form in which it can be understood and identified internationally, according to AACR2R rule 1.4D.
- If there is more than one publisher listed in the publication, only the first will be used in the PDB file. If an online catalog record is used to verify the item, the first place listed there will be used for the name of the publisher. Preference will be given to the cataloging of the Library of Congress, the National Library of Medicine, and the British Library, in that order.

* Ph.D. and other theses:

- Theses are presented in the PUBL record if the degree has been granted and the thesis made available for public consultation by the degree-granting institution.
- The name of the degree-granting institution (the issuing agency) is followed by a space and "(THESIS)".

* Reconstruction of place and publisher:

- The PUBL sub-record type can be reconstructed by removing all trailing blanks in the pub field and concatenating all of the pub fields from the continuation lines with an intervening space. Continued lines do not begin with a space.
COLUMNS    DATA TYPE     FIELD         DEFINITION                                
-------------------------------------------------------------------------------
 1 -  6    Record name   "JRNL  "                                                

13 - 16    LString(4)    "PUBL"                                                  

17 - 18    Continuation  continuation  Allows long publisher and place names.    

20 - 70    LString       pub           City of publication and name of the     
                                       publisher/institution.                    

6. REFN

* REFN is a group of fields which contains encoded references to the citation. No continuation lines are possible. Each piece of coded information has a designated field.

* The American Society for Testing and Materials (ASTM) number is an encoded reference to the journal title. New ASTM codens are assigned by the Chemical Abstracts Service and appear in CASSI and its supplements.

* The country field is blank if the reference was published in more than one country.

* If more than one ISBN is known, select one that matches the individual volume cited (if it happens to be in a set that also has an ISBN for the set). If the reason for multiple ISBNs is that the publication is issued in more than one country, use the ISBN for the country of the first listed place of publication. If there are hardcover and paperback ISBN numbers, use the ISBN for the hardbound version.

* Because some publications do not have an ASTM coden, an ISSN number, or an ISBN number, each publication is assigned a number. This list of numbers, or codens, was established by the Cambridge Crystallographic Data Center (CCDC) and new numbers are assigned by both CCDC and PDB as new publications are added to their respective databases.

* There are two forms of this sub-record type group, depending upon the publication status.

6a. This form of the REFN sub-record type group is used if the citation has not been published.

COLUMNS    DATA TYPE      FIELD      DEFINITION                                   
--------------------------------------------------------------------------------
 1 -  6    Record name    "JRNL  "                                                

13 - 16    LString(4)     "REFN"                                                  

67 - 70    LString(4)     "0353"     This is the CCDC/PDB coden for unpublished 
                                     works.  

6b. This form of the REFN sub-record type group is used if the citation has been published.

COLUMNS    DATA TYPE     FIELD         DEFINITION                                
-------------------------------------------------------------------------------
 1 -  6    Record name   "JRNL  "                                                

13 - 16    LString(4)    "REFN"                                                  

20 - 23    LString(4)    "ASTM"                                                  

25 - 30    LString(6)    astm          ASTM devised coden.                       

33 - 34    LString(2)    country       Country of publication code as defined    
                                       in the OCLC/MARC cataloging format        
                                       (optional).                               

36 - 39    LString(4)    "ISBN" or     International Standard Book Number or     
                         "ISSN"        International Standard Serial Number.     

41 - 65    LString       isbn          ISSN or ISBN number (final digit may be   
                                       a letter and may contain one or more      
                                       dashes).                                  

67 - 70    LString(4)    coden         Code from CCDC/PDB coden list.          

Verification/Validation/Value Authority Control

PDB verifies that this record is correctly formatted.

PDB uses MEDLINE to verify the accuracy of references and to obtain information required for CitDB that is not required by the PDB listing. The process of using MEDLINE requires following the National Library of Medicine rules for the transcription of names and titles. Articles in non-MEDLINE journals are verified through other online databases or with the reprint in hand. Verification of book references is done using online cooperative or individual library catalogs.

Citations appearing in JRNL may not also appear in REMARK 1.

Relationships to Other Record Types

The publication cited as the JRNL record may not be repeated in REMARK 1.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
JRNL        AUTH   N.THANKI,J.K.M.RAO,S.I.FOUNDLING,W.J.HOWE,         
JRNL        AUTH 2 A.G.TOMASSELLI,R.L.HEINRIKSON,S.THAISRIVONGS,      
JRNL        AUTH 3 A.WLODAWER                                         
JRNL        TITL   CRYSTAL STRUCTURE OF A COMPLEX OF HIV-1 PROTEASE   
JRNL        TITL 2 WITH A DIHYDROETHYLENE-CONTAINING INHIBITOR:       
JRNL        TITL 3 COMPARISONS WITH MOLECULAR MODELING                
JRNL        REF    TO BE PUBLISHED                                    
JRNL        REFN                                                  0353

JRNL        AUTH   G.FERMI,M.F.PERUTZ,B.SHAANAN,R.FOURME              
JRNL        TITL   THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 
JRNL        TITL 2 1.74 A RESOLUTION                                  
JRNL        REF    J.MOL.BIOL.                   V. 175   159 1984    
JRNL        REFN   ASTM JMOBAK  UK ISSN 0022-2836                 0070

Known Problems

* Interchange of bibliographic information and linking with other databases is hampered by the lack of labels or specific locations for certain types of information or by more than one type of information being in a particular location. This is most likely to occur with books, series, and reports. Some of the points below provide details about the variations and/or blending of information.

* Titles of the publications that require more than 28 characters on the REF line must be continued on subsequent lines. There is some awkwardness due to volume, page, and year appearing on the first REF line, thereby splitting up the title.

* Information about a supplement and its number/letter is presented in the publication's title field (on the REF lines in columns 20 - 47). This sometimes means that the publication's coden has several versions of REF title information.

* When series information for a book is presented, it is added to the REF line. The number of REF lines can become large in some cases because of the 28-column limit for title information in REF.

* There is often an ISBN for a book title and a separate ISSN for the series in which it was published. There is no way to present more than one of these.

* Books that are issued in more than one series are not accommodated.

* Many books are issued in more than one country. The publisher has a separate ISBN number in each country. There is no place to put any additional applicable ISBN numbers, which would be useful in an international database such as the PDB.

* The country code prefix of the ISBN may not match the country of the place of publication that is listed on the PUBL line when a book is published in more than one country.

* Pagination is limited to the beginning page.

* There is no place for listing a reference's accession number in another database.

* MEDLINE truncates the author list after the tenth name.


REMARK

Overview

REMARK records present experimental details, annotations, comments, and information not included in other records. In a number of cases, REMARKs are used to expand the contents of other record types. A new level of structure is being used for some REMARK records. This is expected to facilitate searching and will assist in the conversion to a relational database.

The very first line of every set of REMARK records is used as a spacer to aid in reading.

COLUMNS      DATA TYPE       FIELD          DEFINITION                           
---------------------------------------------------------------------------------
 1 -  6      Record name     "REMARK"                                            

 8 - 10      Integer         remarkNum      Remark number. It is not an error
                                            for remark n to exist in an entry 
                                            when remark n-1 does not.           

12 - 70      LString         empty          Left as white space in first line of
                                            each new remark.                   

REMARK 1, 2, and 3, detailed below, are specific for references, resolution, and refinement, respectively.

REMARK 1

REMARK 1 lists important publications related to the structure presented in the entry. These citations are chosen by the depositor. They are listed in reverse-chronological order. Citations are not repeated from the JRNL records. After the first blank record and the REFERENCE sub-record, the sub-record types for REMARK 1 are the same as in the JRNL sub-record types. For details, see the JRNL section.

PDB is in the process of linking and/or adding references to CitDB, the literature database of the Genome Data Base (available at URL http://gdbwww.gdb.org/gdb-bin/genera/genera/citation/Citation).

Record Format and Details

As with all other remarks, the first line is empty and is used as a spacer.

The following tables are used to describe the sub-record types of REMARK 1.

1. REFERENCE

Each reference is preceded by a line indicating the reference number in the entry.

COLUMNS        DATA TYPE       FIELD              DEFINITION                     
--------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          

10             LString(1)      "1"                                               

12 - 20        LString(9)      "REFERENCE"                                       

22 - 70        Integer         refNum             Reference number. Starts with 
                                                  1 and increments by 1.        

2. AUTH

AUTH contains the list of authors of the reference.

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
-------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          

10             LString(1)      "1"                                               

13 - 16        LString(4)      "AUTH"         Appears on all continuation        
                                              records.                           

17 - 18        Continuation    continuation   Allows a long list of authors.     

20 - 70        List            authorList     List of the authors.               

See JRNL AUTH for details.

3. TITL

TITL specifies the title of the reference.

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
-------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          

10             LString(1)      "1"                                               

13 - 16        LString(4)      "TITL"         Appears on all continuation        
                                              records.                           

17 - 18        Continuation    continuation   Permits long titles.               

20 - 70        LString         title          Title of the article.              

See JRNL TITL for details.

4. EDIT

EDIT appears if editors are associated with a non-journal reference.

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
-------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          

10             LString(1)      "1"                                               

13 - 16        LString(4)      "EDIT"         Appears on all continuation        
                                              records.                           

17 - 18        Continuation    continuation   Permits long list of editors.      

20 - 70        LString         editorList     List of the editors.               

See JRNL EDIT for details.

5. REF

REF is a group of fields which contains the name of the publication.

5a. If it has not yet been published, the REF sub-record type has the form:

COLUMNS    DATA TYPE      FIELD                   DEFINITION                      
-------------------------------------------------------------------------------
 1 -  6    Record name    "REMARK"                                                

10         LString(1)     "1"                                                     

13 - 16    LString(3)     "REF"                                                   

20 - 34    LString(15)    "TO BE PUBLISHED"                                       

At the present time, there is no formal mechanism in place for monitoring the subsequent publication of referenced papers. PDB relies upon the depositor to provide reference update information since preliminary information can change by the time of actual publication.

5b. If the reference has been published, then the REF sub-record type group contains information about the name of the publication, supplement, report, volume, page, and year, in the appropriate fields.

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
---------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                          

10             LString(1)      "1"                                               

13 - 16        LString(3)      "REF"                                             

17 - 18        Continuation    continuation   Permits long publication names.     

20 - 47        LString         pubName        Name of the publication including  
                                              section or series designation.     
                                              This is the only field of this     
                                              record which may be continued on    
                                              successive records.                 

50 - 51        LString(2)      "V."           Appears in the first record only,   
                                              and only if column 55 is filled in. 

52 - 55        String          volume         Right-justified blank-filled volume 
                                              information; appears in the first   
                                              sub-record only.                    

57 - 61        String          page           First page of the article; appears 
                                              in the first sub-record only.       

63 - 66        Integer         year           Year of publication, first record   
                                              only.                               

See JRNL REF for details.

6. PUBL

PUBL contains the name of the publisher and place of publication if the reference is to a book or other non-journal publication. If the reference has not yet been published or released, this sub-record is absent.

COLUMNS        DATA TYPE       FIELD          DEFINITION                          
---------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                           

10             LString(1)      "1"                                                

13 - 16        LString(4)      "PUBL"                                             

17 - 18        Continuation    continuation   Permits long publisher and city     
                                              information.                        

20 - 70        LString         pub            Name of the publisher and city of   
                                              publication.                        

See JRNL PUBL for details.

7. REFN

REFN is a group of fields which contains encoded references to the citation.

7a. If the citation has not been published, this form of the REFN sub-record type group is used.

COLUMNS    DATA TYPE      FIELD        DEFINITION                                 
-------------------------------------------------------------------------------
 1 -  6    Record name    "REMARK"                                                

10         LString(1)     "1"                                                     

13 - 16    LString(4)     "REFN"                                                  

67 - 70    LString(4)     "0353"       This is the PDB coden for unpublished      
                                       works.                                     

7b. If the citation has been published, this form of the REFN sub-record type group is used.

COLUMNS        DATA TYPE        FIELD            DEFINITION                      
--------------------------------------------------------------------------------
 1 -  6        Record name      "REMARK"                                         

10             LString(1)       "1"                                              

13 - 16        LString(4)       "REFN"                                           

20 - 23        LString(4)       "ASTM"           Blank if reference is not       
                                                 serialized.                     

25 - 30        LString          astm             Code from the ASTM file.        

33 - 34        LString          country          2-digit abbreviation for        
                                                 country of publication.         

36 - 39        LString(4)       "ISBN" or                                        
                                "ISSN"                                           

41 - 65        LString          isbn             ISSN or ISBN number.            

68 - 70        LString(4)       coden            Number from Cambridge           
                                                 Crystallographic Data Center    
                                                 coden list, or assigned by the  
                                                 PDB.                            

See JRNL REFN for details.

Verification/Validation/Value Authority Control

PDB verifies that this record is correctly formatted.

PDB uses MEDLINE to verify the accuracy of references and to obtain information required for CitDB that is not required by the PDB listing. The process of using MEDLINE requires following the National Library of Medicine rules for the transcription of names and titles. Articles in non-MEDLINE journals are verified through other online databases or with the reprint in hand. Verification of book references is done using online cooperative or individual library catalogs.

Citations appearing in REMARK 1 may not appear in JRNL.

Relationships to Other Record Types

Citations appearing in REMARK 1 may not appear in JRNL.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   A.M.BONVIN,J.A.RULLMANN,R.M.LAMERICHS,R.BOELENS,
REMARK   1  AUTH 2 R.KAPTEIN
REMARK   1  TITL   "ENSEMBLE" ITERATIVE RELAXATION MATRIX APPROACH:
REMARK   1  TITL 2 A NEW NMR REFINEMENT PROTOCOL APPLIED TO THE
REMARK   1  TITL 3 SOLUTION STRUCTURE OF CRAMBIN
REMARK   1  REF    PROTEINS: STRUCT.,FUNCT.,     V.  15   385 1993
REMARK   1  REF  2 GENET.
REMARK   1  REFN   ASTM PSFGEY  US ISSN 0887-3585                 0867
REMARK   1 REFERENCE 2
REMARK   1  AUTH   J.A.C.RULLMANN,A.M.J.J.BONVIN,R.BOELENS,R.KAPTEIN
REMARK   1  TITL   STRUCTURE DETERMINATION BY NMR - APPLICATION TO
REMARK   1  TITL 2 CRAMBIN
REMARK   1  EDIT   D.M.SOUMPASIS,T.M.JOVIN
REMARK   1  REF    COMPUTATION OF BIOMOLECULAR              1 1992
REMARK   1  REF  2 STRUCTURES; ACHIEVEMENTS,
REMARK   1  REF  3 PROBLEMS, AND PERSPECTIVES
REMARK   1  PUBL   BERLIN : SPRINGER-VERLAG 
REMARK   1  REFN                GW ISBN 3540559515                2010
REMARK   1 REFERENCE 3
REMARK   1  AUTH   R.M.J.M.LAMERICHS
REMARK   1  REF    2D NMR STUDIES OF                          1989
REMARK   1  REF  2 BIOMOLECULES: PROTEIN 
REMARK   1  REF  3 STRUCTURE AND PROTEIN-DNA 
REMARK   1  REF  4 INTERACTIONS
REMARK   1  PUBL   UTRECHT : UNIVERSITY OF UTRECHT (THESIS)
REMARK   1  REFN                NE                                2011

REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   G.FERMI,M.F.PERUTZ
REMARK   1  REF    HAEMOGLOBIN AND MYOGLOBIN                  1981
REMARK   1  REF  2 (IN: ATLAS OF MOLECULAR
REMARK   1  REF  3 STRUCTURES IN BIOLOGY, V.2)
REMARK   1  PUBL   OXFORD : CLARENDON PRESS
REMARK   1  REFN                   ISBN 0-19-854706-4             0986

Known Problems

See JRNL for a listing of problems associated with references.


REMARK 2

REMARK 2 states the highest resolution, in Angstroms, that was used in building the model. As with all the remarks, the first REMARK 2 record is empty and is used as a spacer.

Record Format and Details

* The second REMARK 2 record has one of two formats. The first is used for diffraction studies, the second for other types of experiments in which resolution is not relevant, e.g., NMR and theoretical modeling.

* For diffraction experiments:

COLUMNS        DATA TYPE       FIELD               DEFINITION                     
--------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                           

10             LString(1)      "2"                                                

12 - 22        LString(11)     "RESOLUTION."                                      

23 - 27        Real(5.2)       resolution          Resolution.                    

29 - 38        LString(10)     "ANGSTROMS."                                       

REMARK 2 when not a diffraction experiment:

COLUMNS        DATA TYPE       FIELD                            DEFINITION        
--------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                           

10             LString(1)      "2"                                                

12 - 38        LString(28)     "RESOLUTION. NOT APPLICABLE."                     

41 - 70        String          comment                          Comment.          

* Additional explanatory text may be included starting with the third line of the REMARK 2 record. For example, depositors may wish to qualify the resolution value provided due to unusual experimental conditions.

COLUMNS        DATA TYPE       FIELD               DEFINITION                     
-------------------------------------------------------------------------------
 1 -  6        Record name     "REMARK"                                           

10             LString(1)      "2"                                                

12 - 22        LString(11)     "RESOLUTION."                                      

24 - 70        String          comment             Comment.                       

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK   2                                                            
REMARK   2 RESOLUTION. 1.74 ANGSTROMS.                                

REMARK   2                                                            
REMARK   2 RESOLUTION. NOT APPLICABLE.                                

REMARK   2                                                            
REMARK   2 RESOLUTION. NOT APPLICABLE.                                
REMARK   2 THIS EXPERIMENT WAS CARRIED OUT USING FLUORESCENCE TRANSFER
REMARK   2 AND THEREFORE NO RESOLUTION CAN BE CALCULATED.


REMARK 3

Overview

REMARK 3 presents information on refinement program(s) used and the related statistics. For non-diffraction studies, REMARK 3 is used to describe any refinement done, but its format in those cases is mostly free text.

If more than one refinement package was used, they may be named in "OTHER REFINEMENT REMARKS". However, Remark 3 statistics are given for the final refinement run.

Refinement packages are being enhanced to output PDB REMARK 3. A token: value template style facilitates parsing. Spacer REMARK 3 lines are interspersed for visually organizing the information.

The templates below have been adopted in consultation with program authors. PDB is continuing this dialogue with program authors, and expects the library of PDB records output by the programs to greatly increase in the near future.

Instead of providing a Record Format table, each template is given as it appears in PDB entries.

Details

* The value "NULL" is given when there is no data available for a particular token.

Refinement using X-PLOR

This remark will be output by X-PLOR(online) for direct submission to PDB. Structures done using earlier versions of X-PLOR will contain the same template, but with many of the data items containing "NULL".

Template

REMARK   3
REMARK   3 REFINEMENT. 
REMARK   3   PROGRAM     : X-PLOR 
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT. 
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 
REMARK   3   NUMBER OF REFLECTIONS             : 
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT. 
REMARK   3   CROSS-VALIDATION METHOD          : 
REMARK   3   FREE R VALUE TEST SET SELECTION  : 
REMARK   3   R VALUE            (WORKING SET) : 
REMARK   3   FREE R VALUE                     : 
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 
REMARK   3   FREE R VALUE TEST SET COUNT      : 
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN. 
REMARK   3   TOTAL NUMBER OF BINS USED           : 
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 
REMARK   3   BIN R VALUE           (WORKING SET) : 
REMARK   3   BIN FREE R VALUE                    : 
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. 
REMARK   3   PROTEIN ATOMS            : 
REMARK   3   NUCLEIC ACID ATOMS       : 
REMARK   3   HETEROGEN ATOMS          : 
REMARK   3   SOLVENT ATOMS            : 
REMARK   3
REMARK   3  B VALUES. 
REMARK   3   FROM WILSON PLOT           (A**2) : 
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 
REMARK   3   OVERALL ANISOTROPIC B VALUE. 
REMARK   3    B11 (A**2) : 
REMARK   3    B22 (A**2) : 
REMARK   3    B33 (A**2) : 
REMARK   3    B12 (A**2) : 
REMARK   3    B13 (A**2) : 
REMARK   3    B23 (A**2) : 
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR. 
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 
REMARK   3   ESD FROM SIGMAA              (A) : 
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR. 
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 
REMARK   3   ESD FROM C-V SIGMAA          (A) : 
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES. 
REMARK   3   BOND LENGTHS                 (A) : 
REMARK   3   BOND ANGLES            (DEGREES) : 
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 
REMARK   3   IMPROPER ANGLES        (DEGREES) : 
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : 
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) :       ; 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) :       ; 
REMARK   3   SIDE-CHAIN BOND              (A**2) :       ; 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) :       ; 
REMARK   3
REMARK   3  NCS MODEL : 
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) :       ; 
REMARK   3   GROUP  1  B-FACTOR           (A**2) :       ; 
REMARK   3   GROUP  2  POSITIONAL            (A) :       ; 
REMARK   3   GROUP  2  B-FACTOR           (A**2) :       ; 
REMARK   3   GROUP  3  POSITIONAL            (A) :       ; 
REMARK   3   GROUP  3  B-FACTOR           (A**2) :       ; 
REMARK   3   GROUP  4  POSITIONAL            (A) :       ; 
REMARK   3   GROUP  4  B-FACTOR           (A**2) :       ; 
REMARK   3
REMARK   3  PARAMETER FILE  1  : 
REMARK   3  PARAMETER FILE  2  : 
REMARK   3  PARAMETER FILE  3  : 
REMARK   3  PARAMETER FILE  4  : 
REMARK   3  PARAMETER FILE  5  : 
REMARK   3  PARAMETER FILE  6  : 
REMARK   3  TOPOLOGY FILE  1   : 
REMARK   3  TOPOLOGY FILE  2   : 
REMARK   3  TOPOLOGY FILE  3   : 
REMARK   3  TOPOLOGY FILE  4   : 
REMARK   3  TOPOLOGY FILE  5   : 
REMARK   3  TOPOLOGY FILE  6   : 
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: 

Refinement using NUCLSQ

Template

REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : NUCLSQ
REMARK   3   AUTHORS     : WESTHOF,DUMAS,MORAS 
REMARK   3
REMARK   3  DATA USED IN REFINEMENT. 
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 
REMARK   3   COMPLETENESS FOR RANGE        (%) : 
REMARK   3   NUMBER OF REFLECTIONS             : 
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : 
REMARK   3   FREE R VALUE TEST SET SELECTION  : 
REMARK   3   R VALUE     (WORKING + TEST SET) :
REMARK   3   R VALUE            (WORKING SET) :
REMARK   3   FREE R VALUE                     :
REMARK   3   FREE R VALUE TEST SET SIZE   (%) :
REMARK   3   FREE R VALUE TEST SET COUNT      :
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) :
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) :
REMARK   3   FREE R VALUE                  (NO CUTOFF) :
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 
REMARK   3  
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            :
REMARK   3   NUCLEIC ACID ATOMS       :
REMARK   3   HETEROGEN ATOMS          :
REMARK   3   SOLVENT ATOMS            :
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 
REMARK   3    B22 (A**2) : 
REMARK   3    B33 (A**2) : 
REMARK   3    B12 (A**2) : 
REMARK   3    B13 (A**2) : 
REMARK   3    B23 (A**2) : 
REMARK   3  
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 
REMARK   3   ESD FROM SIGMAA              (A) : 
REMARK   3   LOW RESOLUTION CUTOFF        (A) :
REMARK   3 
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   DISTANCE RESTRAINTS.                    RMS     SIGMA
REMARK   3    SUGAR-BASE BOND DISTANCE        (A) :       ; 
REMARK   3    SUGAR-BASE BOND ANGLE DISTANCE  (A) :       ; 
REMARK   3    PHOSPHATE BONDS DISTANCE        (A) :       ;  
REMARK   3    PHOSPHATE BOND ANGLE, H-BOND    (A) :       ; 
REMARK   3 
REMARK   3   PLANE RESTRAINT                  (A) :       ;  
REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) :       ;  
REMARK   3 
REMARK   3   NON-BONDED CONTACT RESTRAINTS. 
REMARK   3    SINGLE TORSION CONTACT          (A) :       ;  
REMARK   3    MULTIPLE TORSION CONTACT        (A) :       ;  
REMARK   3 
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA 
REMARK   3   SUGAR-BASE BONDS             (A**2) :       ;  
REMARK   3   SUGAR-BASE ANGLES            (A**2) :       ;  
REMARK   3   PHOSPHATE BONDS              (A**2) :       ;  
REMARK   3   PHOSPHATE BOND ANGLE, H-BOND (A**2) :       ;  
REMARK   3 
REMARK   3  OTHER REFINEMENT REMARKS: 

Refinement using PROLSQ, CCP4, PROFFT, GPRLSA, and related programs

Template

REMARK   3 
REMARK   3 REFINEMENT. 
REMARK   3   PROGRAM     : 
REMARK   3   AUTHORS     : 
REMARK   3 
REMARK   3  DATA USED IN REFINEMENT.  
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) :  
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) :  
REMARK   3   DATA CUTOFF            (SIGMA(F)) :  
REMARK   3   COMPLETENESS FOR RANGE        (%) :  
REMARK   3   NUMBER OF REFLECTIONS             :  
REMARK   3 
REMARK   3  FIT TO DATA USED IN REFINEMENT. 
REMARK   3   CROSS-VALIDATION METHOD          : 
REMARK   3   FREE R VALUE TEST SET SELECTION  : 
REMARK   3   R VALUE     (WORKING + TEST SET) : 
REMARK   3   R VALUE            (WORKING SET) : 
REMARK   3   FREE R VALUE                     : 
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 
REMARK   3   FREE R VALUE TEST SET COUNT      : 
REMARK   3 
REMARK   3  FIT/AGREEMENT OF MODEL WITH ALL DATA. 
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 
REMARK   3   FREE R VALUE                  (NO CUTOFF) :  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) :  
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) :  
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) :  
REMARK   3   
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. 
REMARK   3   PROTEIN ATOMS            : 
REMARK   3   NUCLEIC ACID ATOMS       : 
REMARK   3   HETEROGEN ATOMS          : 
REMARK   3   SOLVENT ATOMS            : 
REMARK   3 
REMARK   3  B VALUES. 
REMARK   3   FROM WILSON PLOT           (A**2) :  
REMARK   3   MEAN B VALUE      (OVERALL, A**2) :  
REMARK   3   OVERALL ANISOTROPIC B VALUE. 
REMARK   3    B11 (A**2) :  
REMARK   3    B22 (A**2) :  
REMARK   3    B33 (A**2) :  
REMARK   3    B12 (A**2) :  
REMARK   3    B13 (A**2) :  
REMARK   3    B23 (A**2) :  
REMARK   3   
REMARK   3  ESTIMATED COORDINATE ERROR. 
REMARK   3   ESD FROM LUZZATI PLOT        (A) :  
REMARK   3   ESD FROM SIGMAA              (A) :  
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 
REMARK   3  
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES. 
REMARK   3   DISTANCE RESTRAINTS.                    RMS    SIGMA 
REMARK   3    BOND LENGTH                     (A) :       ;  
REMARK   3    ANGLE DISTANCE                  (A) :       ; 
REMARK   3    INTRAPLANAR 1-4 DISTANCE        (A) :       ;  
REMARK   3    H-BOND OR METAL COORDINATION    (A) :       ;  
REMARK   3 
REMARK   3   PLANE RESTRAINT                  (A) :       ;  
REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) :       ;  
REMARK   3 
REMARK   3   NON-BONDED CONTACT RESTRAINTS. 
REMARK   3    SINGLE TORSION                  (A) :       ;  
REMARK   3    MULTIPLE TORSION                (A) :       ;  
REMARK   3    H-BOND (X...Y)                  (A) :       ;  
REMARK   3    H-BOND (X-H...Y)                (A) :       ;  
REMARK   3 
REMARK   3   CONFORMATIONAL TORSION ANGLE RESTRAINTS. 
REMARK   3    SPECIFIED                 (DEGREES) :       ;  
REMARK   3    PLANAR                    (DEGREES) :       ;  
REMARK   3    STAGGERED                 (DEGREES) :       ;  
REMARK   3    TRANSVERSE                (DEGREES) :       ;  
REMARK   3 
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA 
REMARK   3   MAIN-CHAIN BOND              (A**2) :       ;  
REMARK   3   MAIN-CHAIN ANGLE             (A**2) :       ;  
REMARK   3   SIDE-CHAIN BOND              (A**2) :       ;  
REMARK   3   SIDE-CHAIN ANGLE             (A**2) :       ;  
REMARK   3 
REMARK   3  OTHER REFINEMENT REMARKS: 

Refinement using SHELXL
This remark will be output by SHELXL-96 for direct submission to PDB. Structures done using earlier versions of SHELX will use the same template, but with many of the data items containing "NULL".

Template

REMARK   3
REMARK   3 REFINEMENT.
REMARK   3  PROGRAM     : SHELXL
REMARK   3  AUTHORS     : G.M.SHELDRICK
REMARK   3
REMARK   3 DATA USED IN REFINEMENT.
REMARK   3  RESOLUTION RANGE HIGH (ANGSTROMS) : 
REMARK   3  RESOLUTION RANGE LOW  (ANGSTROMS) :
REMARK   3  DATA CUTOFF            (SIGMA(F)) : 
REMARK   3  COMPLETENESS FOR RANGE        (%) :
REMARK   3  CROSS-VALIDATION METHOD           : 
REMARK   3  FREE R VALUE TEST SET SELECTION   : 
REMARK   3
REMARK   3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK   3  R VALUE   (WORKING + TEST SET, NO CUTOFF) : 
REMARK   3  R VALUE          (WORKING SET, NO CUTOFF) : 
REMARK   3  FREE R VALUE                  (NO CUTOFF) : 
REMARK   3  FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 
REMARK   3  FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 
REMARK   3  TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 
REMARK   3
REMARK   3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3  R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 
REMARK   3  R VALUE          (WORKING SET, F>4SIG(F)) : 
REMARK   3  FREE R VALUE                  (F>4SIG(F)) : 
REMARK   3  FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 
REMARK   3  FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : 
REMARK   3  TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 
REMARK   3
REMARK   3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3  PROTEIN ATOMS      : 
REMARK   3  NUCLEIC ACID ATOMS : 
REMARK   3  HETEROGEN ATOMS    : 
REMARK   3  SOLVENT ATOMS      : 
REMARK   3
REMARK   3 MODEL REFINEMENT.
REMARK   3  OCCUPANCY SUM OF NON-HYDROGEN ATOMS      :
REMARK   3  OCCUPANCY SUM OF HYDROGEN ATOMS          : 
REMARK   3  NUMBER OF DISCRETELY DISORDERED RESIDUES : 
REMARK   3  NUMBER OF LEAST-SQUARES PARAMETERS       : 
REMARK   3  NUMBER OF RESTRAINTS                     : 
REMARK   3
REMARK   3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3  BOND LENGTHS                         (A) : 
REMARK   3  ANGLE DISTANCES                      (A) : 
REMARK   3  SIMILAR DISTANCES (NO TARGET VALUES) (A) : 
REMARK   3  DISTANCES FROM RESTRAINT PLANES      (A) : 
REMARK   3  ZERO CHIRAL VOLUMES               (A**3) : 
REMARK   3  NON-ZERO CHIRAL VOLUMES           (A**3) : 
REMARK   3  ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 
REMARK   3  RIGID-BOND ADP COMPONENTS         (A**2) : 
REMARK   3  SIMILAR ADP COMPONENTS            (A**2) :
REMARK   3  APPROXIMATELY ISOTROPIC ADPS      (A**2) : 
REMARK   3
REMARK   3 BULK SOLVENT MODELING.
REMARK   3  METHOD USED: 
REMARK   3
REMARK   3 STEREOCHEMISTRY TARGET VALUES : 
REMARK   3  SPECIAL CASE:
REMARK   3
REMARK   3 OTHER REFINEMENT REMARKS:

Refinement using TNT

Template

REMARK   3 
REMARK   3 REFINEMENT. 
REMARK   3   PROGRAM     : TNT  
REMARK   3   AUTHORS     : TRONRUD,TEN EYCK,MATTHEWS 
REMARK   3 
REMARK   3  DATA USED IN REFINEMENT.  
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) :
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) :
REMARK   3   DATA CUTOFF            (SIGMA(F)) :
REMARK   3   COMPLETENESS FOR RANGE        (%) : 
REMARK   3   NUMBER OF REFLECTIONS             : 
REMARK   3 
REMARK   3  USING DATA ABOVE SIGMA CUTOFF. 
REMARK   3   CROSS-VALIDATION METHOD          :  
REMARK   3   FREE R VALUE TEST SET SELECTION  :  
REMARK   3   R VALUE     (WORKING + TEST SET) : 
REMARK   3   R VALUE            (WORKING SET) : 
REMARK   3   FREE R VALUE                     : 
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 
REMARK   3   FREE R VALUE TEST SET COUNT      : 
REMARK   3 
REMARK   3  USING ALL DATA, NO SIGMA CUTOFF. 
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 
REMARK   3   FREE R VALUE                  (NO CUTOFF) :  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) :  
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) :  
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) :  
REMARK   3 
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. 
REMARK   3   PROTEIN ATOMS            :  
REMARK   3   NUCLEIC ACID ATOMS       :  
REMARK   3   OTHER ATOMS          :  
REMARK   3 
REMARK   3  WILSON B VALUE (FROM FCALC, A**2) :  
REMARK   3 
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.    RMS    WEIGHT  COUNT 
REMARK   3   BOND LENGTHS                 (A) :       ;       ;  
REMARK   3   BOND ANGLES            (DEGREES) :       ;       ;  
REMARK   3   TORSION ANGLES         (DEGREES) :       ;       ;  
REMARK   3   PSEUDOROTATION ANGLES  (DEGREES) :       ;       ;  
REMARK   3   TRIGONAL CARBON PLANES       (A) :       ;       ;  
REMARK   3   GENERAL PLANES               (A) :       ;       ;  
REMARK   3   ISOTROPIC THERMAL FACTORS (A**2) :       ;       ;  
REMARK   3   NON-BONDED CONTACTS          (A) :       ;       ;  
REMARK   3 
REMARK   3  INCORRECT CHIRAL-CENTERS (COUNT) :  
REMARK   3 
REMARK   3  BULK SOLVENT MODELING. 
REMARK   3   METHOD USED :  
REMARK   3   KSOL        :  
REMARK   3   BSOL        :  
REMARK   3 
REMARK   3  RESTRAINT LIBRARIES. 
REMARK   3   STEREOCHEMISTRY :  
REMARK   3   ISOTROPIC THERMAL FACTOR RESTRAINTS :  
REMARK   3 
REMARK   3  OTHER REFINEMENT REMARKS: 

Non-diffraction studies
Until standard refinement remarks are adopted for non-diffraction studies, their refinement details are given in REMARK 3, but its format will consist totally of free text beginning on the sixth line of the remark.

Template

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK   3 
REMARK   3 REFINEMENT.                                                
REMARK   3   PROGRAM     : 
REMARK   3   AUTHORS     : 
REMARK   3                                                            
REMARK   3 FREE TEXT                                     

Example

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REMARK   3 
REMARK   3 REFINEMENT.                                                
REMARK   3   PROGRAM     : X-PLOR 3.1                    
REMARK   3   AUTHORS     : BRUNGER                       
REMARK   3                                                            
REMARK   3 STRUCTURAL STATISTICS:                                     
REMARK   3                                      25 SA                 
REMARK   3                                      STRUCTURES  SAAVEMIN  
REMARK   3  RMS DEVIATIONS FROM EXP. RESTRAINTS[A]                    
REMARK   3   NOE DISTANCE RESTRAINTS (1430)   0.0451 A       0.044 A  
REMARK   3   DIHEDRAL ANGLE RESTRAINTS (130)  0.551 DEG      0.660 DEG
REMARK   3  DEVIATIONS FROM IDEAL GEOMETRY                            
REMARK   3   BONDS                            0.004  A       0.004 A  
REMARK   3   ANGLES                           0.661 DEG      0.650 DEG
REMARK   3   IMPROPERS                        0.371 DEG      0.380 DEG
REMARK   3  X-PLOR ENERGIES (IN KCAL MOL-1)[B]                        
REMARK   3   ENOE                             167            158      
REMARK   3   ECDIH                            2.6            3.4      
REMARK   3   ENCS                             0.01           0.01     
REMARK   3   EREPEL                           54             50       
REMARK   3   EBOND                            36             33       
REMARK   3   EANGLE                           263            256      
REMARK   3   EIMPROPER                        22             23       
REMARK   3   ETOTAL                           545            523      
REMARK   3  ATOMIC RMS DIFFERENCES[C]                                 
REMARK   3  BACKBONE(N, CA, C') + LIGAND ATOMS   0.53+/-0.09 A        
REMARK   3  ALL HEAVY ATOMS                      0.91+/-0.08 A        

REMARK 4 - 999

Overview

REMARKs following the refinement remark consist of free text annotation, predefined boilerplate remarks, and token: value pair styled templates. PDB is beginning to organize the most often used remarks, and assign numbers and topics to them.

Presented here is the scheme being followed in the remark section of PDB files. The PDB expects to continue to adopt standard text or tables for certain remarks, as details are worked out.

Record Format and Details

* Non-standard remark annotations, or those with no clearly-defined topic or assigned remark number, appear with remark number 6 or greater, but less than remark number 100.

* Note that A, B, N, X, Y, and Z are used to represent variables in the following examples.

* As with all other remarks, the first line of each remark is empty and is used as a spacer.

REMARK 4, Format

Entries released after April 15, 1996 will comply with Format Version 2.0, described in this document. Conversion of older entries to this format will begin in the fall of 1996.
Entries conforming to the format described in this or future PDB Contents Guides will have a remark of the following form within them:
Remark 4 is mandatory in entry if released after April 15, 1996.

Template

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REMARK   4
REMARK   4 XXXX COMPLIES WITH FORMAT V. N.M, DD-MMM-YYYY

XXXX refers to the ID code of the entry.
N.M refers to the version number.
DD-MMM-YYYY refers to the release date of that version of the format. DD is a number 01 through 31, MMM is a 3 letter abbreviation for the month, and YYYY is the year.

Example

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REMARK   4
REMARK   4 1ABC COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996

REMARK 5, Warning

Remark 5 repeats information presented on the CAVEAT record, which warns of severe errors in an entry. It also presents depositors' remarks of a cautionary nature, such as noting regions of poorly defined density.

Template

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REMARK   5
REMARK   5 WARNING
REMARK   5 XXXX: FREE TEXT GOES HERE.

XXXX refers to the ID code of the entry.

Example

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REMARK   5
REMARK   5 WARNING
REMARK   5 1ABC: THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS
REMARK   5 UNCORRECTABLE AT THIS TIME.

REMARK 6 - 99, not assigned

Non-standard remark annotations, or those with no clearly defined topic or assigned remark number appear with remark number 6 or greater, but less than remark number 100.

REMARK 100 - 199, Nucleic acids

These remarks are used in nucleic acid structures processed by the Nucleic Acid Database.

Template

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REMARK 100 
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY THE NUCLEIC ACID DATABASE  
REMARK 100 ON DD-MMM-YYYY. 
REMARK 100 THE NDB ID CODE IS NNNNNN. 

For modified residues

Remark 101 is mandatory if substituted nucleic acid residues exit.

Template

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REMARK 101
REMARK 101 RESIDUE   X Y   N HAS XXX    BONDED TO AB. 
REMARK 101 RESIDUE   X Y   N HAS XXX    BONDED TO AB. 

X is the modified residue name, Y is the chain identifier, N is the sequence number, XXX is the name of the modifier, A is the atom name and B the sequence number of the atom carrying the modifier.

Example

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REMARK 101
REMARK 101 RESIDUE   G A   4 HAS CH3    BONDED TO O6.
REMARK 101 RESIDUE   G B  16 HAS CH3    BONDED TO O6.

For base mispairings

Remark 102 is mandatory if mispaired bases exist and Watson-Crick H-bonding is present.

Template

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REMARK 102
REMARK 102 BASES   A B  NN AND   X Y  ZZ ARE MISPAIRED. 
REMARK 102 BASES   A B  NN AND   X Y  ZZ ARE MISPAIRED. 
REMARK 102 ALL OTHER HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
REMARK 102 FOLLOW THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
REMARK 102 PATTERN AND THEY HAVE NOT BEEN PRESENTED ON *CONECT*
REMARK 102 RECORDS IN THIS ENTRY. 

A is the residue name, B the chain identifier, and NN the sequence number of first base, X is the residue name, Y the chain id, and ZZ the sequence number of the second base.

Example

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REMARK 102
REMARK 102 BASES   G A   4 AND   A B  21 ARE MISPAIRED. 
REMARK 102 BASES   A A   9 AND   G B  16 ARE MISPAIRED. 
REMARK 102 ALL OTHER HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
REMARK 102 FOLLOW THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
REMARK 102 PATTERN AND THEY HAVE NOT BEEN PRESENTED ON *CONECT*
REMARK 102 RECORDS IN THIS ENTRY. 

For structures containing inosine

Inosine is treated like a standard residue, however, entries containing inosine also include remarks 103 and 104.

Remark 103 is mandatory if non-Watson-Crick H-bonding is present for specific interactions.

Template

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REMARK 103
REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE
REMARK 103 FOLLOWING ATOMS: 
REMARK 103  AB   I X   N   AND  AB   Z X  NN
REMARK 103  AB   I X   N   AND  AB   Z X  NN
REMARK 103 ALL OTHER HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
REMARK 103 FOLLOW THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
REMARK 103 PATTERN AND THEY HAVE NOT BEEN PRESENTED ON *CONECT*
REMARK 103 RECORDS IN THIS ENTRY. 

AB is the atom name, I the residue name inosine, X the chain identifier, and N the sequence number of inosine, and AB is the atom name, Z the residue name, X the chain identifier, and NN the sequence number of the base which is paired with inosine.

Remark 104 is mandatory if inosine exists.

Template

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REMARK 104
REMARK 104 RESIDUE I X   N IS INOSINE. 
REMARK 104 RESIDUE I X   N IS INOSINE. 

X is the chain identifier and N the sequence number.

Example

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REMARK 103
REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE
REMARK 103 FOLLOWING ATOMS: 
REMARK 103  N1   I A   1   AND  N3   C B  16
REMARK 103  O6   I A   1   AND  N4   C B  16
REMARK 103  N1   I A   3   AND  N3   C B  14
REMARK 103  O6   I A   3   AND  N4   C B  14
REMARK 103 ALL OTHER HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
REMARK 103 FOLLOW THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
REMARK 103 PATTERN AND THEY HAVE NOT BEEN PRESENTED ON CONECT
REMARK 103 RECORDS IN THIS ENTRY.
REMARK 104
REMARK 104 RESIDUE I A   1 IS INOSINE. 
REMARK 104 RESIDUE I A   3 IS INOSINE. 

For nucleic acid entries

Remark 105 is mandatory if nucleic acids exist in an entry.

Template

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REMARK 105 
REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS  
REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY    
REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS.  THE RING     
REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.

For non-mismatched structures

Remark 106 is mandatory if hydrogen bonding is Watson-Crick.

Template

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REMARK 106
REMARK 106 THE HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY FOLLOW
REMARK 106 THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING PATTERN.
REMARK 106 THEY HAVE NOT BEEN PRESENTED ON *CONECT* RECORDS IN THIS
REMARK 106 ENTRY.

REMARK 200-250, Experimental Details

Remarks in this range present the data collection details for the data which resulted in the refinement statistics of REMARK 3. They provide information on the structure determination experiment, which may have been done by diffraction, NMR, theoretical modelling, or some other technique.
The "NULL" value will be used if the data for a token is not supplied by the depositor.

REMARK 200, X-ray Diffraction Experimental Details

To be used for single crystal, fiber, or polycrystalline X-ray diffraction experiments.
Remark 200 is mandatory if x-ray.

Template

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REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 
REMARK 200  TEMPERATURE           (KELVIN) : 
REMARK 200  PH                             : 
REMARK 200  NUMBER OF CRYSTALS USED        : 
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : 
REMARK 200  RADIATION SOURCE               : 
REMARK 200  BEAMLINE                       : 
REMARK 200  X-RAY GENERATOR MODEL          : 
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : 
REMARK 200  WAVELENGTH OR RANGE        (A) : 
REMARK 200  MONOCHROMATOR                  : 
REMARK 200  OPTICS                         : 
REMARK 200
REMARK 200  DETECTOR TYPE                  : 
REMARK 200  DETECTOR MANUFACTURER          : 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : 
REMARK 200  DATA SCALING SOFTWARE          : 
REMARK 200  
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 
REMARK 200  RESOLUTION RANGE HIGH      (A) : 
REMARK 200  RESOLUTION RANGE LOW       (A) : 
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 
REMARK 200  DATA REDUNDANCY                : 
REMARK 200  R MERGE                    (I) : 
REMARK 200  R SYM                      (I) : 
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 
REMARK 200  COMPLETENESS FOR SHELL     (%) : 
REMARK 200  DATA REDUNDANCY IN SHELL       : 
REMARK 200  R MERGE FOR SHELL          (I) : 
REMARK 200  R SYM FOR SHELL            (I) : 
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 
REMARK 200
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: 
REMARK 200 SOFTWARE USED: 
REMARK 200 STARTING MODEL: 
REMARK 200
REMARK 200 REMARK:  

Remark 205, Fiber Diffraction, Fiber Sample Experiment Details

Remark 205 is mandatory if fiber diffraction - non-crystalline sample.

Template

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REMARK 205
REMARK 205 THESE COORDINATES WERE GENERATED FROM FIBER DIFFRACTION
REMARK 205 DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1
REMARK 205 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES OF THESE
REMARK 205 RECORDS ARE MEANINGLESS. 

Remarks 210 and 215, NMR Experiment Details

Remark 210 is mandatory if NMR.

Template

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REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) :
REMARK 210  PH                             :
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      :
REMARK 210  SPECTROMETER FIELD STRENGTH    :
REMARK 210  SPECTROMETER MODEL             :
REMARK 210  SPECTROMETER MANUFACTURER      :
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 :
REMARK 210   METHOD USED                   :
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   :
REMARK 210 CONFORMERS, NUMBER SUBMITTED    :
REMARK 210 CONFORMERS, SELECTION CRITERIA  :
REMARK 210
REMARK 210 REMARK: 

Remark 215 is mandatory if NMR

Template

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REMARK 215                                                              
REMARK 215 NMR STUDY                                                    
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION   
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT        
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON      
REMARK 215 THESE RECORDS ARE MEANINGLESS. 

Remarks 220 and 225, Theoretical Modelling Experiment Details

Remark 220 is mandatory if theoretical model.

Template

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REMARK 220
REMARK 220 EXPERIMENTAL DETAILS
REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING
REMARK 220
REMARK 220 REMARK: 

Remark 225 is mandatory if theoretical model.

Template

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REMARK 225
REMARK 225 THEORETICAL MODEL
REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE.
REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND
REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE
REMARK 225 RECORDS ARE MEANINGLESS.

Remark 230, Neutron Diffraction Experiment Details

Remark 230 is mandatory if neutron diffraction study.

Template

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REMARK 230
REMARK 230 EXPERIMENTAL DETAILS
REMARK 230  EXPERIMENT TYPE                : NEUTRON DIFFRACTION
REMARK 230  DATE OF DATA COLLECTION        :
REMARK 230  TEMPERATURE           (KELVIN) :
REMARK 230  PH                             :
REMARK 230  NUMBER OF CRYSTALS USED        :
REMARK 230
REMARK 230  NEUTRON SOURCE                 :
REMARK 230  BEAMLINE                       :
REMARK 230  WAVELENGTH OR RANGE        (A) :
REMARK 230  MONOCHROMATOR                  :
REMARK 230  OPTICS                         :
REMARK 230
REMARK 230  DETECTOR TYPE                  :
REMARK 230  DETECTOR MANUFACTURER          :
REMARK 230  INTENSITY-INTEGRATION SOFTWARE :
REMARK 230  DATA SCALING SOFTWARE          :
REMARK 230
REMARK 230  NUMBER OF UNIQUE REFLECTIONS   :
REMARK 230  RESOLUTION RANGE HIGH      (A) :
REMARK 230  RESOLUTION RANGE LOW       (A) :
REMARK 230  REJECTION CRITERIA  (SIGMA(I)) :
REMARK 230
REMARK 230 OVERALL.
REMARK 230  COMPLETENESS FOR RANGE     (%) :
REMARK 230  DATA REDUNDANCY                :
REMARK 230  R MERGE                    (I) : 
REMARK 230  R SYM                      (I) : 
REMARK 230  <I/SIGMA(I)> FOR THE DATA SET  :
REMARK 230
REMARK 230 IN THE HIGHEST RESOLUTION SHELL.
REMARK 230  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :
REMARK 230  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) :
REMARK 230  COMPLETENESS FOR SHELL     (%) :
REMARK 230  DATA REDUNDANCY IN SHELL       :
REMARK 230  R MERGE FOR SHELL          (I) : 
REMARK 230  R SYM FOR SHELL            (I) : 
REMARK 230  <I/SIGMA(I)> FOR SHELL         :
REMARK 230
REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE:
REMARK 230 SOFTWARE USED :
REMARK 230 STARTING MODEL:
REMARK 230
REMARK 230 REMARK: 

Remark 240, Electron Diffraction Experiment Details

Remark 240 is mandatory if electron diffraction study.

Template

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REMARK 240
REMARK 240 EXPERIMENTAL DETAILS 
REMARK 240  EXPERIMENT TYPE                : ELECTRON DIFFRACTION
REMARK 240  DATE OF DATA COLLECTION        : 
REMARK 240
REMARK 240 REMARK: 

Remark 250, Other Type of Experiment Details

Remark specific to other kinds of studies, not listed above.
Remark 250 is mandatory if other than x-ray, NMR, theoretical model, neutron, or electron study.

Template

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REMARK 250
REMARK 250 EXPERIMENTAL DETAILS 
REMARK 250  EXPERIMENT TYPE                :
REMARK 250  DATE OF DATA COLLECTION        : 
REMARK 250
REMARK 250 REMARK: 

REMARK 280, Crystal

Remark 280 presents information on the crystal. The solvent content and Matthews coefficient are provided for protein and polypeptide crystals. Crystallization conditions are free text.
Remark 280 is mandatory if single crystal study.

Template

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REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%):
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: FREE TEXT GOES HERE.

REMARK 285, CRYST1

Remark 285 presents information on the unit cell.

Template

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REMARK 285
REMARK 285 CRYST1
REMARK 285 FREE TEXT GOES HERE. 

Example

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REMARK 285                                                            
REMARK 285 CRYST1                                                     
REMARK 285 TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA:  THE DATA WAS      
REMARK 285 COLLECTED ON TWO-DIMENSIONAL CRYSTALS AND HENCE THE        
REMARK 285 C-AXIS REPEAT DOES NOT CORRESPOND TO A REAL REPEAT, BUT    
REMARK 285 INSTEAD REFERS TO THE SAMPLING THAT IS USED TO DESCRIBE    
REMARK 285 THE CONTINUOUS TRANSFORM.  THE C VALUE OF 100.9 IS         
REMARK 285 THEREFORE THE VALUE WHICH SHOULD BE USED IN                
REMARK 285 INTERPRETING THE MEANING OF THE L INDEX. 

REMARK 290, Crystallographic Symmetry

Remark 290 is mandatory for crystalline studies. The remark is generated by PDB.

Template

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REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                  
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21             
REMARK 290                                                            
REMARK 290      SYMOP   SYMMETRY                                      
REMARK 290     NNNMMM   OPERATOR                                      
REMARK 290       1555   X,Y,Z                                         
REMARK 290       2555   1/2-X,-Y,1/2+Z                                
REMARK 290       3555   -X,1/2+Y,1/2-Z                                
REMARK 290       4555   1/2+X,1/2-Y,-Z                                
REMARK 290                                                            
REMARK 290     WHERE NNN -> OPERATOR NUMBER                           
REMARK 290           MMM -> TRANSLATION VECTOR                        
REMARK 290                                                            
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                  
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM   
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY      
REMARK 290 RELATED MOLECULES. 
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000  
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       36.30027  
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       59.50256  
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       59.50256  
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       36.30027  
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000  
REMARK 290                                                            
REMARK 290 REMARK:                                                

Example

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REMARK 290
REMARK 290                                                            
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                  
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21             
REMARK 290                                                            
REMARK 290      SYMOP   SYMMETRY                                      
REMARK 290     NNNMMM   OPERATOR                                      
REMARK 290       1555   X,Y,Z                                         
REMARK 290       2555   1/2-X,-Y,1/2+Z                                
REMARK 290       3555   -X,1/2+Y,1/2-Z                                
REMARK 290       4555   1/2+X,1/2-Y,-Z                                
REMARK 290                                                           
REMARK 290     WHERE NNN -> OPERATOR NUMBER                           
REMARK 290           MMM -> TRANSLATION VECTOR                       
REMARK 290                                                            
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                  
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM   
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY      
REMARK 290 RELATED MOLECULES. 
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000  
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       36.30027  
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000  
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       59.50256  
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000  
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       59.50256  
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       36.30027 
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       46.45545  
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000  
REMARK 290                                                            
REMARK 290 REMARK: NULL                                               

REMARK 295, Non-Crystallographic Symmetry

Description of non-crystallographic symmetry. Mandatory when MTRIX records are present.

Template

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REMARK 295
REMARK 295 NON-CRYSTALLOGRAPHIC SYMMETRY
REMARK 295 THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW
REMARK 295 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS
REMARK 295 IN THIS ENTRY.  APPLYING THE APPROPRIATE MTRIX 
REMARK 295 TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD
REMARK 295 APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND.
REMARK 295 CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH
REMARK 295 ATOMS ARE NOT FOUND IN THIS ENTRY.  
REMARK 295
REMARK 295               APPLIED TO          TRANSFORMED TO
REMARK 295   TRANSFORM CHAIN  RESIDUES       CHAIN  RESIDUES     RMSD
REMARK 295     SSS       ?    ? .. ?           ?    ? .. ?       ?
REMARK 295
REMARK 295    WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS
REMARK 295
REMARK 295 REMARK: 

Example

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REMARK 295
REMARK 295 NON-CRYSTALLOGRAPHIC SYMMETRY
REMARK 295 THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW
REMARK 295 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS
REMARK 295 IN THIS ENTRY.  APPLYING THE APPROPRIATE MTRIX 
REMARK 295 TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD
REMARK 295 APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND.
REMARK 295 CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH
REMARK 295 ATOMS ARE NOT FOUND IN THIS ENTRY.  
REMARK 295
REMARK 295               APPLIED TO          TRANSFORMED TO
REMARK 295   TRANSFORM CHAIN  RESIDUES       CHAIN  RESIDUES     RMSD
REMARK 295     SSS
REMARK 295    M  1       A    1 .. 374         C    1 .. 374     0.010
REMARK 295    M  2       B    1 .. 374         D    1 .. 374     0.010
REMARK 295
REMARK 295    WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS
REMARK 295
REMARK 295 REMARK: 

REMARK 300, Biomolecule

Description of the biologically functional molecule (biomolecule) in free text.
Remark 300 is mandatory if Remark 350 is provided.

Template

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REMARK 300
REMARK 300 BIOMOLECULE
REMARK 300 FREE TEXT DESCRIPTION OF THE BIOLOGICALLY FUNCTIONAL 
REMARK 300 MOLECULE.

Example

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REMARK 300
REMARK 300 BIOMOLECULE
REMARK 300 THE CATALYTIC SUBUNIT OF LIVER ALCOHOL DEHYDROGENASE FROM
REMARK 300 EQUUS CABALLUS IS A HOMO DIMER. 

REMARK 350, Generating the Biomolecule

Remark 350 presents all transformations, both crystallographic and non-crystallographic, needed to generate the biomolecule. These transformations operate on the coordinates in the entry.
Remark 350 is mandatory if Remark 300 is provided.

Template

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REMARK 350  
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN 
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND 
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. 
REMARK 350
REMARK 350 APPLY THE FOLLOWING TO CHAINS: ?, ?...
REMARK 350   BIOMT1   N  N.NNNNNN  N.NNNNNN  N.NNNNNN        N.NNNNN
REMARK 350   BIOMT2   N  N.NNNNNN  N.NNNNNN  N.NNNNNN        N.NNNNN
REMARK 350   BIOMT3   N  N.NNNNNN  N.NNNNNN  N.NNNNNN        N.NNNNN 

Example

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REMARK 350  
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN 
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND 
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. 
REMARK 350
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000       60.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000     -120.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F
REMARK 350   BIOMT1   3  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   3  0.000000 -1.000000  0.000000       60.00000
REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   4 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   4  0.000000 -1.000000  0.000000     -120.00000
REMARK 350   BIOMT3   4  0.000000  0.000000  1.000000        0.00000

REMARK 350  
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN 
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND 
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. 
REMARK 350
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H
REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J, K, L
REMARK 350   BIOMT1   1 -0.500000 -0.865983  0.000000        0.00000
REMARK 350   BIOMT2   1  0.866068 -0.500000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000

REMARK 375, Special Position

Remark 375 specifies atoms that are known to lie in particular locations, related by the symmetry elements, at which objects may be placed if and only if they possess symmetry which coincides with that of the cell.

Template

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REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 FREE TEXT GOES HERE. 

Example

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REMARK 375                                                            
REMARK 375 SPECIAL POSITION                                           
REMARK 375      HOH   301  LIES ON A SPECIAL POSITION.                 
REMARK 375      HOH    77  LIES ON A SPECIAL POSITION.                 

REMARK 375                                                         
REMARK 375 SPECIAL POSITION                                        
REMARK 375 MG   MO4 A  10  LIES ON A SPECIAL POSITION.              
REMARK 375      HOH A  13  LIES ON A SPECIAL POSITION.              
REMARK 375      HOH A  28  LIES ON A SPECIAL POSITION.              
REMARK 375      HOH A  36  LIES ON A SPECIAL POSITION.              

REMARK 400, Compound

Further details on the macromolecular contents of the entry.

Template

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REMARK 400
REMARK 400 COMPOUND
REMARK 400 FREE TEXT GOES HERE.

REMARK 450, Source

Further details on the biological source of the macromolecular contents of the entry.

Template

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REMARK 450
REMARK 450 SOURCE
REMARK 450 FREE TEXT GOES HERE.

REMARK 460, Non-IUPAC Names

Remark 460 is mandatory when IUPAC-IUB rules are not strictly followed in naming side-chain atoms.

Template

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REMARK 460
REMARK 460 NON-IUPAC
REMARK 460 BY REQUEST OF THE DEPOSITOR, THE PROTEIN DATA BANK HAS NOT
REMARK 460 APPLIED THE IUPAC-IUB RECOMMENDATIONS REGARDING THE
REMARK 460 DESIGNATION OF BRANCHES 1 AND 2 OF SIDE-CHAIN ATOMS IN
REMARK 460 RESIDUES ARG, ASP, GLU, LEU, PHE, TYR, AND VAL TO THIS
REMARK 460 ENTRY. 

REMARK 470, Missing Atom

Non-hydrogen atoms of standard residues which are missing from the coordinates are listed. Missing HETATMS are not listed here.

Template

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REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;  
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; 
REMARK 470 I=INSERTION CODE):                                          
REMARK 470   M RES CSSEQI  ATOMS                                       

Example

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REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;  
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; 
REMARK 470 I=INSERTION CODE):                                          
REMARK 470   M RES CSSEQI  ATOMS                                       
REMARK 470     ARG A 412    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     ARG A 456    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     GLU A 486    CG   CD   OE1  OE2                         
REMARK 470     GLU A 547    CG   CD   OE1  OE2                         
REMARK 470     GLU A 548    CG   CD   OE1  OE2                         
REMARK 470     LYS A 606    CG   CD   CE   NZ                          
REMARK 470     ARG B 456    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     ASP B 484    CG   OD1  OD2                              
REMARK 470     GLN B 485    CG   CD   OE1  NE2                         
REMARK 470     GLU B 486    CG   CD   OE1  OE2                         
REMARK 470     ARG B 490    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     GLU B 522    CG   CD   OE1  OE2                         
REMARK 470     ARG B 576    CG   CD   NE   CZ   NH1  NH2               
REMARK 470     ASP B 599    CG   OD1  OD2

REMARK 500, Geometry and Stereochemistry

Further details on the stereochemistry of the structure. This remark is generated by PDB, but may also be provided by the depositor. Additional subtopics may be added as needed.

Template

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY 
REMARK 500 SUBTOPIC: 
REMARK 500 
REMARK 500 FREE TEXT GOES HERE.

Example, close contacts

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC 
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  SOME OF THESE MAY BE ATOMS
REMARK 500 LOCATED ON SPECIAL POSITIONS IN THE CELL.
REMARK 500
REMARK 500 DISTANCE CUTOFF: 2.2 ANGSTROMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   CB   LEU D    68  -  CE   LYS E    76     1656     2.10
REMARK 500   CB   THR D   173  -  O    HOH    1151     4455     1.73
REMARK 500   O    HOH    1151  -  CB   THR D   173     4566     1.73
REMARK 500   CZ   ARG D    64  -  O    HOH    1422     3656     1.75 

REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   O    HOH     761  -  O    ARG      17              1.89
REMARK 500   O    HOH     806  -  N    ARG      88              1.46

Example, non-CIS, non-trans

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500                                 MODEL     OMEGA
REMARK 500 VAL A  123    GLN A  124          0       221.48
REMARK 500 VAL B  123    GLN B  124          0       222.43

Example, chiral centers

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE: 
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,A12)
REMARK 500
REMARK 500  M RES CSSEQI
REMARK 500  0 GLU     1       ALPHA-CARBON
REMARK 500  0 GLU     1       SIDE-CHAIN
REMARK 500  0 GLU     1       ALPHA-CARBON

Example, covalent bond angles

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 4*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(2X,A4,17X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500  0 ASP     3   C-1 -  N   -  CA  ANGL. DEV. =  21.7 DEGREES

Example, torsion angles

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REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES 
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; 
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE: 
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500  0 VAL    26     -174.85   -134.80
REMARK 500  0 MET    61       46.11   -176.53

REMARK 525, Solvent

Remarks specific to the solvent molecules of the entry.

Template

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REMARK 525
REMARK 525 SOLVENT
REMARK 525 FREE TEXT GOES HERE. 

Example

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REMARK 525
REMARK 525 SOLVENT
REMARK 525 MANY OF THE WATER MOLECULES APPEAR TO BE ASSOCIATED WITH
REMARK 525 A SYMMETRY-RELATED MOLECULE. 

REMARK 525
REMARK 525 SOLVENT
REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED
REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE
REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL
REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525 
REMARK 525  M RES CSSEQI                                            
REMARK 525  0 HOH    561      DISTANCE =  5.07 ANGSTROMS            
REMARK 525  0 HOH    791      DISTANCE =  5.08 ANGSTROMS

REMARK 550, SEGID

Description of the segment identifiers used in ATOM/HETATM.

Template

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REMARK 550
REMARK 550 SEGID
REMARK 550 FREE TEXT GOES HERE.

Example

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REMARK 550
REMARK 550 SEGID
REMARK 550 RESIDUES 1-55, SEGID VH1 ARE THE HEAVY CHAIN, VARIABLE 
REMARK 550 REGION 1.  RESIDUES 56-100, SEGID VH2 ARE THE HEAVY CHAIN, 
REMARK 550 VARIABLE REGION 2,AND RESIDUES 101-150., SEGID VH3 ARE THE 
REMARK 550 HEAVY CHAIN.

REMARK 600, Heterogen

Further details on the heterogens in the entry.

Template

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REMARK 600
REMARK 600 HETEROGEN
REMARK 600 FREE TEXT GOES HERE.

Example

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REMARK 600                                                            
REMARK 600 HETEROGEN                                                  
REMARK 600 HET GROUP TRIVIAL NAME: PHOSPHOTYROSINE                    
REMARK 600 EMPIRICAL FORMULA     : C9 O6 N P                          
REMARK 600                                                            
REMARK 600                O                                           
REMARK 600               /                           _                
REMARK 600          O = C           C = C           O                 
REMARK 600               \         /     \         /   _              
REMARK 600                C - C - C       C - O - P - O               
REMARK 600               /         \\   //        \\                  
REMARK 600              N           C - C           O                 
REMARK 600                                                            
REMARK 600                                                            
REMARK 600 NUMBER OF ATOMS IN GROUP: 17 (EXCLUDING HYDROGENS) 

REMARK 650, Helix

Further details on the helix contents of the entry.

Template

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REMARK 650
REMARK 650 HELIX
REMARK 650 FREE TEXT GOES HERE.

Example

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REMARK 650                                                            
REMARK 650 HELIX                                                      
REMARK 650 DETERMINATION METHOD: KDSSP                                
REMARK 650 THE MAJOR DOMAINS ARE: "N" FOR N-TERMINAL DOMAIN, "B" FOR  
REMARK 650 BETA-BARREL DOMAIN, AND "C" FOR C-TERMINAL DOMAIN. "F"     
REMARK 650 REFERS TO THE ACTIVE SITE FLAP.  ALPHA HELICES ARE NAMED   
REMARK 650 WITH TWO CHARACTERS, THE FIRST REFERRING TO THE DOMAIN     
REMARK 650 IN WHICH THEY OCCUR. 

REMARK 700, Sheet

Further details on the sheet contents of the structure. Several standard templates are included here.

Template

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REMARK 700
REMARK 700 SHEET
REMARK 700 FREE TEXT GOES HERE. 

REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD:                                 
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED.  IN
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, 
REMARK 700 TWO SHEETS ARE DEFINED.  STRANDS N1, N2, N3 AND N4 OF SHEET
REMARK 700 XXX AND XXX ARE IDENTICAL. 

REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD:                                 
REMARK 700 THE SHEET PRESENTED AS XXX ON SHEET RECORDS BELOW IS
REMARK 700 ACTUALLY AN N-STRANDED BETA-BARREL.  THIS IS
REMARK 700 REPRESENTED BY A N+1-STRANDED SHEET IN WHICH THE FIRST AND
REMARK 700 LAST STRANDS ARE IDENTICAL. 

REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD:                                 
REMARK 700 THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. 
REMARK 700 EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE
REMARK 700 IDENTICAL STRANDS. 
REMARK 700 SHEETS XXX AND XXX REPRESENT ONE BIFURCATED SHEET. 
REMARK 700 SHEETS XXX AND XXX REPRESENT ONE BIFURCATED SHEET. 

N1, N2, N3 and N4 represent strand numbers, and XXX represents sheet identifiers.

When the remark for several bifurcated sheets is used, its last line is repeated for the appropriate number of bifurcated sheets, as shown in the last template above.

Example

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REMARK 700
REMARK 700 SHEET
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED.  IN   
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
REMARK 700 TWO SHEETS are defined.  STRANDS 3, 4, AND 5 
REMARK 700 OF SHEET *B2A* AND *B2B* ARE IDENTICAL.  STRANDS 3, 4, AND
REMARK 700 5 OF SHEET *B2C* AND *B2D* ARE IDENTICAL.                 

REMARK 700                                                           
REMARK 700 SHEET
REMARK 700 STRANDS 1 TO 4 OF THE BETA-SHEET HAVE GREEK-KEY TOPOLOGY. 
REMARK 700 THE SHEET FORMS A FIVE-STRANDED BETA-BARREL WITH BULGES IN 
REMARK 700 STRANDS 3 AND 5.  IN ORDER TO REPRESENT THIS FEATURE IN THE
REMARK 700 SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.               

REMARK 700                                                            
REMARK 700 SHEET                                                      
REMARK 700 THE SHEET PRESENTED AS S5 ON SHEET RECORDS BELOW IS        
REMARK 700 ACTUALLY A 6-STRANDED BETA-BARREL.  THIS IS                
REMARK 700 REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND   
REMARK 700 LAST STRANDS ARE IDENTICAL.                                

REMARK 750, Turn

Further details on the turns.

Template

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REMARK 750
REMARK 750 TURN
REMARK 750 FREE TEXT GOES HERE.

Example

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REMARK 750
REMARK 750 TURN
REMARK 750  TURN_ID: T4, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES    
REMARK 750  DEVIATE BY MORE THAN PLUS,MINUS 45 DEGREES FROM THE IDEAL  
REMARK 750  VALUES USED BY WILMOT & THORNTON(1989)). 
REMARK 750                                                             
REMARK 750  TURN_ID: T10, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES   
REMARK 750  DEVIATE BY MORE THAN PLUS,MINUS 45 DEGREES FROM THE IDEAL  
REMARK 750  VALUES USED BY WILMOT & THORNTON(1989)). 
REMARK 750                                                             
REMARK 750  TURN_ID: T16, TYPE VIII (ONE OR MORE OF THE PHI, PSI       
REMARK 750  ANGLES DEVIATE BY MORE THAN PLUS,MINUS 45 DEGREES FROM     
REMARK 750  THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). 

REMARK 800, Site

Further details on the site contents of the entry.
Remark 800 is mandatory if site records exist.

Template

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REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: FREE TEXT GOES HERE. 
REMARK 800 SITE_DESCRIPTION: FREE TEXT GOES HERE.

Example

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REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: RCA
REMARK 800 SITE_DESCRIPTION: DESIGNATED RECOGNITION REGION IN PRIMARY
REMARK 800 REFERENCE.  PROPOSED TO AFFECT SUBSTRATE SPECIFICITY.      
REMARK 800
REMARK 800 SITE_IDENTIFIER: RCB                                       
REMARK 800 SITE_DESCRIPTION: DESIGNATED RECOGNITION REGION IN PRIMARY 
REMARK 800  REFERENCE.  PROPOSED TO AFFECT SUBSTRATE SPECIFICITY.     
 

REMARK 850, Revisions to Deposited Coordinates, Before Release

Template

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REMARK 850
REMARK 850 CORRECTION BEFORE RELEASE
REMARK 850 ORIGINAL DEPOSITION REVISED PRIOR TO RELEASE
REMARK 850 DATE REVISED: DD-MMM-YYYY  TRACKING NUMBER: T?

DD is a number 01 through 31, MMM is a 3 letter abbreviation for the month, and YYYY is the year.

Example

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REMARK 850                                                         
REMARK 850 CORRECTION BEFORE RELEASE                               
REMARK 850 ORIGINAL DEPOSITION REVISED PRIOR TO RELEASE            
REMARK 850 DATE REVISED: 13-FEB-1996  TRACKING NUMBER: T7770       
REMARK 850 DATE REVISED: 10-APR-1996  TRACKING NUMBER: T8125       

REMARK 860, Correction, After Release

Further details on corrections that have been made to the PDB entry, as referred to in the REVDAT record.

Template

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1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 860
REMARK 860 CORRECTION AFTER RELEASE
REMARK 860 FREE TEXT GOES HERE. 

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 860
REMARK 860 CORRECTION
REMARK 860 CORRECT RESIDUE IDENTIFICATION ON SITE RECORDS.  ADD       
REMARK 860 RESIDUE TO SITE RECORDS.  15-JUL-81.                       
REMARK 860                                                            
REMARK 860 CORRECT DATES IN REMARKS 7 AND 16. 15-JAN-82.    
REMARK 860                                                            
REMARK 860 CORRECT ATOM NAME FOR ATOM 6 FROM CG2 TO CG1.  07-MAR-83.  
REMARK 860                                                            
REMARK 860 CHANGE RESIDUE 122 FROM ASN TO ASP.  ADD REFERENCE.        
REMARK 860  12-MAY-83.                                      
REMARK 860                                                            
REMARK 860 INSERT REVDAT RECORDS. 30-SEP-83.              
REMARK 860                                                            
REMARK 860 CORRECT CODEN FOR REFERENCE 1.  27-OCT-83.     

REMARK 900, Related Entries

This remark gives ID codes of PDB files related to the entry. These may include coordinate entries deposited as a related set, the structure factor or NMR restraint file related to the entry, or the file containing the biologically functional molecule ("biomolecule") generated by the PDB from symmetry records.

Template

         1         2         3         4         5         6         7
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REMARK 900 
REMARK 900 RELATED ENTRIES
REMARK 900 FREE TEXT GOES HERE.

Example

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1234567890123456789012345678901234567890123456789012345678901234567890
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 THE BIOMOLECULE RELATED TO THIS ENTRY HAS BEEN GENERATED
REMARK 900 AND IS AVAILABLE AS PDB FILE BIO1ABC.PDB

REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 THE STRUCTURE FACTORS FOR THIS EXPERIMENT ARE AVAILABLE AS
REMARK 900 PDB FILE R1ABCSF.ENT

REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 THE LIST OF EXPERIMENTAL RESTRAINTS IS AVAILABLE AS PDB
REMARK 900 FILE 1ABC.MR

REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 THE BIOMOLECULE IS AVAILABLE AS PDB FILE BIO1ABC.PDB

REMARK 999 Sequence

Further details on the sequence.

For cases where there are gaps in the structure as reflected in missing ATOM records missing N-terminus and C-terminus residues are delineated in REMARK 999 records, whereas internal structural gaps are represented in SEQADV records. Several cases must be considered when evaluating these REMARK 999 records:

1. The missing N-terminus atoms are not found in the ATOM record as they represent precursor sequence and are not found in the mature protein.
2. The missing N-terminus residues were not found in the density map. Although PDB will attempt to flag these as SEQADV records, we cannot guarantee that they will always be handled uniformly. The primary reason for this inconsistency is that in a number of cases, neither PDB nor the depositors, are certain where chains start and end.

Template

         1         2         3         4         5         6         7
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REMARK 999
REMARK 999 SEQUENCE
REMARK 999 FREE TEXT GOES HERE.

Example

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REMARK 999                                                            
REMARK 999 SEQUENCE                                                   
REMARK 999 1ARL       SWS     P00730       1 -   110 NOT IN ATOMS LIST
REMARK 999 1ARL       SWS     P00730     418 -   419 NOT IN ATOMS LIST
REMARK 999                                                            
REMARK 999  REFERENCE                                                 
REMARK 999   REFERENCE: PETRA, ET AL., (1971) BIOCHEMISTRY 10, PP     
REMARK 999   4023-4025.                                               
REMARK 999                                                            
REMARK 999   SHOHAM, G., NECHUSHTAI, R., STEPPUN, J.,NELSON, H.,      
REMARK 999   NELSON N., UNPUBLISHED RESULTS.                          
REMARK 999                                                            
REMARK 999   LE HUEROU,I., GUILLOTEAU P., TOULLEC, R., PUIGSERVER, A.,
REMARK 999   WICKER,C., (1991) BIOCHEMICAL, BIOPHYSICAL RESEARCH      
REMARK 999   COMM., 175, PP 110 - 116.                                
REMARK 999                                                            
REMARK 999 THE SEQUENCE USED IS THAT PROVIDED BY THE CDNA, WHICH      
REMARK 999 CORRECTS SEVERAL ASP/ASN AND GLU/GLN MISASSIGNMENTS.       

REMARK 999                                                            
REMARK 999 SEQUENCE                                                   
REMARK 999 MET A    1  - MET A    1  - MISSING FROM SWS    P10599     
REMARK 999 1CQG  B    SWS     P27695       1 -    57 NOT IN ATOMS LIST
REMARK 999 1CQG  B    SWS     P27695      71 -   317 NOT IN ATOMS LIST
REMARK 999                                                            
REMARK 999 THR AT POSITION 74 WAS FOUND BY WOLMAN ET AL., JOURNAL OF  
REMARK 999 BIOCHEMISTRY 263, 15506 (1988).                            



3. Primary Structure Section

The primary structure section of a PDB file contains the sequence of residues in each chain of the macromolecule. Embedded in these records are chain identifiers and sequence numbers that allow other records to link into the sequence.


DBREF

Overview

The DBREF record provides cross-reference links between PDB sequences and the corresponding database entry or entries. A cross reference to the sequence database is mandatory for each peptide chain with a length greater than ten (10) residues. For nucleic acid entries a DBREF record pointing to the Nucleic Acid Database (NDB) is mandatory when the corresponding entry exists in NDB.

Record Format

COLUMNS       DATA TYPE       FIELD          DEFINITION                            
--------------------------------------------------------------------------------
 1 -  6       Record name     "DBREF "                                          

 8 - 11       IDcode          idCode         ID code of this entry.             

13            Character       chainID        Chain identifier.                  

15 - 18       Integer         seqBegin       Initial sequence number of the PDB 
                                             sequence segment.                  

19            AChar           insertBegin    Initial insertion code of the PDB  
                                             sequence segment.                  

21 - 24       Integer         seqEnd         Ending sequence number of the PDB  
                                             sequence segment.                  

25            AChar           insertEnd      Ending insertion code of the PDB   
                                             sequence segment.                  

27 - 32       LString         database       Sequence database name.  "PDB" when
                                             a corresponding sequence database  
                                             entry has not been identified.     

34 - 41       LString         dbAccession    Sequence database accession code.  
                                             For GenBank entries, this is the   
                                             NCBI gi number.                    

43 - 54       LString         dbIdCode       Sequence database identification   
                                             code.  For GenBank entries, this is
                                             the accession code.                

56 - 60       Integer         dbseqBegin     Initial sequence number of the     
                                             database seqment.                  

61            AChar           idbnsBeg       Insertion code of initial residue  
                                             of the segment, if PDB is the      
                                             reference.                         

63 - 67       Integer         dbseqEnd       Ending sequence number of the      
                                             database segment.                  

68            AChar           dbinsEnd       Insertion code of the ending       
                                             residue of the segment, if PDB is  
                                             the reference.

Details

* PDB entries contain multi-chain molecules with sequences that may be wild type, variant, or synthetic. Sequences may also have been modified through site-directed mutagenesis experiments (engineered). A number of PDB entries report structures of domains cleaved from larger molecules.

* The DBREF record was designed to account for these differences by providing explicit correlations between contiguous segments of sequences as given in the PDB ATOM records and the sequence database entry. Several cases are easily represented by means of pointers between the databases using DBREF. PDB entries containing heteropolymers are linked to different sequence database entries. In some cases, such as those PDB entries containing immunoglobulin Fab fragments, each chain is linked to two different SWISS-PROT, PIR, and/or GenBank entries. This facility is needed because these databases represent sequences for the various immunoglobulin domains as separate entries. DBREF also is able to represent molecules engineered by altering the gene (fusing genes, altering sequences, creating chimeras, or circularly permuting sequences). This design has the additional advantage that it will be possible to construct pointers to other relevant databases such as the Nucleic Acid Database, BioMagResBank, and databases describing sequence motifs (e.g., PROSITE, BLOCKS).

* Database names and their abbreviations as used on DBREF records.

   Database name                            database (code in columns 27 - 32)
   ---------------------------------------------------------------------------
   BioMagResBank                            BMRB
   BLOCKS                                   BLOCKS
   European Molecular Biology Laboratory    EMBL
   GenBank                                  GB
   Genome Data Base                         GDB
   Nucleic Acid Database                    NDB
   PROSITE                                  PROSIT
   Protein Data Bank                        PDB
   Protein Identification Resource          PIR
   SWISS-PROT                               SWS
   TREMBL                                   TREMBL

* When no sequence numbers are given (columns 15 - 25 and 56 - 68), then the mapping is between database entries rather than segments within an entry. For example, this is normally used to point to the related NDB entry.

* DBREF records present sequence correlations between PDB ATOM records and corresponding PIR, GenBank, or SWISS-PROT, etc. entries.

* PDB does not guarantee that all possible references to the listed databases will be provided. In most cases, only one reference to a sequence database will be provided.

* PDB entries containing chains for which residues are missing primarily due to disorder contain several DBREF records, each linking an observed sequence segment to a sequence database entry.

* If no reference is found in the sequence databases, then the PDB entry itself is given as the reference.

* For nucleic acid entries a DBREF record pointing to the Nucleic Acid Database (NDB) is mandatory when the corresponding entry exists in NDB.

* Selection of the appropriate sequence database entry or entries to be linked to a PDB entry is done on the basis of the sequence and its biological source. Questions on entry assignment that may arise are resolved by consultation with database staff.

Verification/Validation/Value Authority Control

The sequence database entry found during PDB's search is compared to that provided by the depositor and any differences are resolved or annotated.

In most cases, only one reference to a sequence database will be provided. PDB does not guarantee that all possible references to the listed databases will be provided.

Relationships to Other Record Types

DBREF represents the sequence as found in ATOM and HETATM records.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
DBREF  1ABC B    1B   36  PDB    1ABC     1ABC             1B    36

DBREF  3AKY      3   220  SWS    P07170   KAD1_YEAST       5    222 

DBREF  1HAN      2   288  GB     397884   X66122           1    287 

DBREF  3HSV A    1    92  SWS    P22121   HSF_KLULA      193    284
DBREF  3HSV B    1    92  SWS    P22121   HSF_KLULA      193    284

DBREF  1ARL      1   307  SWS    P00730   CBPA_BOVIN     111    417  

DBREF  249D A    1    12  NDB    BDL070   BDL070           1     12   
DBREF  249D B   13    24  NDB    BDL070   BDL070          13     24   
DBREF  249D C   26    36  NDB    BDL070   BDL070          26     36   
DBREF  249D D   37    48  NDB    BDL070   BDL070          37     48   


SEQADV

Overview

The SEQADV record identifies conflicts between sequence information in the ATOM records of the PDB entry and the sequence database entry given on DBREF. Please note that these records were designed to identify differences and not errors. No assumption is made as to which database contains the correct data. PDB may include REMARK records in the entry that reflect the depositor's view of which database has the correct sequence.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                          
----------------------------------------------------------------------------------
 1 -  6        Record name     "SEQADV"                                           

 8 - 11        IDcode          idCode         ID code of this entry.              

13 - 15        Residue name    resName        Name of the PDB residue in conflict.

17             Character       chainID        PDB chain identifier.               

19 - 22        Integer         seqNum         PDB sequence number.                

23             AChar           iCode          PDB insertion code.                 

25 - 28        LString         database       Sequence database name.             

30 - 38        LString         dbIdCode       Sequence database accession     
                                              number.                             

40 - 42        Residue name    dbRes          Sequence database residue name.     

44 - 48        Integer         dbSeq          Sequence database sequence number.  

50 - 70        LString         conflict       Conflict comment.                

Details

* For cases where there are gaps in the structure as reflected in missing ATOM records, SEQADV records are produced which reflect the lack of correlation between the chain and the sequence database entry. (Several DBREF records are also produced.) Note that internal structural gaps are represented in SEQADV records, whereas missing N-terminus and C-terminus residues are delineated in REMARK 999 records

* If the missing N-terminus residues were not found in the density map, the PDB will attempt to flag these as SEQADV records. However, we cannot guarantee that they will always be handled uniformly since, in a number of cases, neither PDB nor the depositors are certain where chains start and end.

* In a number of cases, conflicts between the sequences found in PDB entries and in PIR or SWISS-PROT entries have been noted. There are several possible reasons for these conflicts, including natural variants or engineered sequences (mutants), polymorphic sequences, or ambiguous or conflicting experimental results. These discrepancies, which were previously described in REMARK records, are now reported in SEQADV.

* SEQADV describes conflicts between residue sequences given by PDB ATOM/HETATM records and those in the appropriate sequence database entry, such as residues missing due to disorder.

* This record will give a description of the differences between the sequence database entries and complete chains. If a chain is referenced by more than one sequence database entry, as in the case of fused genes, then SEQADV will describe the relationship between each chain segment.

* Some of the possible conflict comments:

Cloning artifact
Conflict
Engineered
Disordered
Gap in PDB entry
Missing from [database name]
Variant
Insertion
Deletion
Microheterogeneity
D-configuration

* When conflicts arise which are not classifiable by these terms, a reference to either a published paper, a PDB entry, or a REMARK within the entry is given. References are given in the form YY-VOL-PAGE-CODEN where YY is year of publication, VOL is the journal volume number, PAGE is the starting page and CODEN is the 4-digit code assigned to journals by PDB and the Cambridge Crystallographic Data Centre (CCDC).

* When reference is made to a PDB entry, then the form is PDB: 1ABC, where 1ABC is the relevant entry ID code.

* Finally, the comment "SEE REMARK 999" is included when the explanation for the conflict is too long to fit the SEQADV record.

* Microheterogeneity is to be represented as a variant with one of the possible residues in the site being selected (arbitrarily) as the primary residue, in which case a SEQADV record must be provided for the alternate residue.

Verification/Validation/Value Authority Control

SEQADV records are automatically generated by the PDB.

Relationships to Other Record Types

SEQADV refers to the sequence as found in the ATOM and HETATM records, and to the sequence database reference found on DBREF.

REMARK 999 contains text explaining discrepancies when the explanation is too lengthy to fit in SEQADV.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SEQADV 1ABC ASN A  100A SWS  P10725    ASP   100 1994-300-1200-0070

SEQADV 2ABC ASN A  100A SWS  P10725    ASP   100 PDB: 1ABC

SEQADV 3ABC MET A   -1  SWS  P10725              CLONING ARTIFACT
SEQADV 3ABC GLY A   50  SWS  P10725    VAL    50 ENGINEERED


SEQRES

Overview

SEQRES records contain the amino acid or nucleic acid sequence of residues in each chain of the macromolecule that was studied.

Record Format

COLUMNS        DATA TYPE       FIELD         DEFINITION                           
---------------------------------------------------------------------------------
 1 -  6        Record name     "SEQRES"                                           

 9 - 10        Integer         serNum        Serial number of the SEQRES record   
                                             for the current chain.  Starts at 1  
                                             and increments by one each line.     
                                             Reset to 1 for each chain.           

12             Character       chainID       Chain identifier.  This may be any   
                                             single legal character, including a  
                                             blank which is used if there is      
                                             only one chain.                      

14 - 17        Integer         numRes        Number of residues in the chain.     
                                             This value is repeated on every      
                                             record.                              

20 - 22        Residue name    resName       Residue name.                        

24 - 26        Residue name    resName       Residue name.                        

28 - 30        Residue name    resName       Residue name.                        

32 - 34        Residue name    resName       Residue name.                        

36 - 38        Residue name    resName       Residue name.                        

40 - 42        Residue name    resName       Residue name.                        

44 - 46        Residue name    resName       Residue name.                        

48 - 50        Residue name    resName       Residue name.                        

52 - 54        Residue name    resName       Residue name.                        

56 - 58        Residue name    resName       Residue name.                        

60 - 62        Residue name    resName       Residue name.                        

64 - 66        Residue name    resName       Residue name.                        

68 - 70        Residue name    resName       Residue name.                        

Details

* PDB entries use the three-letter abbreviation for amino acid names and the one letter code for nucleic acids.

* In the case of non-standard groups, a hetID of up to three (3) alphanumeric characters is used. Common HET names appear in the HET dictionary.

* Each covalently contiguous sequence of residues (connected via the "backbone" atoms) is represented as an individual chain.

* Heterogens which are integrated into the backbone of the chain are listed as being part of the chain and are included in the SEQRES records for that chain.

* Each set of SEQRES records and each HET group is assigned a component number. The component number is assigned serially beginning with 1 for the first set of SEQRES records. This number is given explicitly in the FORMUL record, but only implicitly in the SEQRES record.

* The SEQRES records must list residues present in the molecule studied, even if the coordinates are not present.

* C- and N-terminus residues for which no coordinates are provided due to disorder must be listed on SEQRES.

* All occurrences of standard amino or nucleic acid residues (ATOM records) must be listed on a SEQRES record. This implies that a numRes of 1 is valid.

* No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U, I).

* If the entire residue sequence is unknown, the serNum in column 10 is "0", the number of residues thought to comprise the molecule is entered as numRes in columns 14 - 17, and resName in columns 20 - 22 is "UNK".

* In case of microheterogeneity, only one of the sequences is presented. A REMARK is generated to explain this and a SEQADV is also generated.

Verification/Validation/Value Authority Control

The residues presented on the SEQRES records must agree with those found in the ATOM records.

The SEQRES records are checked by PDB using the sequence databases and information provided by the depositor.

SEQRES is compared to the ATOM records during processing, and both are checked against the sequence database. All discrepancies are either resolved or annotated in the entry.

Relationships to Other Record Types

The residues presented on the SEQRES records must agree with those found in the ATOM records. DBREF refers to the corresponding entry in the sequence databases. SEQADV lists all discrepancies between the entry's sequence for which there are coordinates and that referenced in the sequence database. MODRES describes modifications to a standard residue.

Example

         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SEQRES   1 A   21  GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU
SEQRES   2 A   21  TYR GLN LEU GLU ASN TYR CYS ASN                    
SEQRES   1 B   30  PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU
SEQRES   2 B   30  ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR
SEQRES   3 B   30  THR PRO LYS ALA                                    
SEQRES   1 C   21  GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU
SEQRES   2 C   21  TYR GLN LEU GLU ASN TYR CYS ASN                    
SEQRES   1 D   30  PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU
SEQRES   2 D   30  ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR
SEQRES   3 D   30  THR PRO LYS ALA                                    

Known Problems

Polysaccharides do not lend themselves to being represented in SEQRES.

There is no mechanism provided to describe sequence runs when the exact ordering of the sequence is not known.

For cyclic peptides, PDB arbitrarily assigns a residue as the N-terminus.

For microheterogeneity only one of the possible residues in a given position is provided in SEQRES.

No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U).


MODRES

Overview

The MODRES record provides descriptions of modifications (e.g., chemical or post-translational) to protein and nucleic acid residues. Included are a mapping between residue names given in a PDB entry and standard residues.

Record Format

COLUMNS        DATA TYPE       FIELD          DEFINITION                         
--------------------------------------------------------------------------------
 1 -  6        Record name     "MODRES"                                          

 8 - 11        IDcode          idCode         ID code of this entry.             

13 - 15        Residue name    resName        Residue name used in this entry.   

17             Character       chainID        Chain identifier.                  

19 - 22        Integer         seqNum         Sequence number.                   

23             AChar           iCode          Insertion code.                    

25 - 27        Residue name    stdRes         Standard residue name.             

30 - 70        String          comment        Descrip