This section contains records used to describe the experiment and the biological macromolecules present in the entry: HEADER, OBSLTE, TITLE, SPLIT, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRNL, and REMARK records.
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 when the coordinates were deposited to the PDB archive.
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 at the PDB. 63 - 66 IDcode idCode This identifier is unique within the PDB.
Details
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. "No coordinates", or NOC files, given as 0xxx codes, contained no structural information and were bibliographic only. These entries were subsequently removed from PDB archive.
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 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 HEADER PHOTOSYNTHESIS 28-MAR-07 2UXK HEADER TRANSFERASE/TRANSFERASE INHIBITOR 17-SEP-04 1XH6 HEADER MEMBRANE PROTEIN, TRANSPORT PROTEIN 20-JUL-06 2HRT
Overview
OBSLTE appears in entries that have been removed from public distribution.
This record acts as a flag in an entry that has been removed ("obsoleted") from the PDB's full release. It indicates which, if any, new entries have replaced the entry that was obsoleted. 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. 72 - 75 IDcode rIdCode ID code of entry that replaced this one.
Details
Verification/Validation/Value Authority Control
wwPDB staff adds 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 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
OBSLTE 31-JAN-94 1MBP 2MBP
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 same way that a citation title identifies a publication.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------------------- 1 - 6 Record name "TITLE " 9 - 10 Continuation continuation Allows concatenation of multiple records. 11 - 80 String title Title of the experiment.
Details
- 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 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).
Examples
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
TITLE RHIZOPUSPEPSIN COMPLEXED WITH REDUCED PEPTIDE INHIBITOR
TITLE STRUCTURE OF THE TRANSFORMED MONOCLINIC LYSOZYME BY
TITLE 2 CONTROLLED DEHYDRATION
TITLE NMR STUDY OF OXIDIZED THIOREDOXIN MUTANT (C62A,C69A,C73A)
TITLE 2 MINIMIZED AVERAGE STRUCTURE
Overview
The SPLIT record is used in instances where a specific entry composes part of a large macromolecular complex. It will identify the PDB entries that are required to reconstitute a complete complex.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------------------- 1 - 6 Record name "SPLIT " 9 - 10 Continuation continuation Allows concatenation of multiple records. 12 - 15 IDcode idCode ID code of related entry. 17 - 20 IDcode idCode ID code of related entry. 22 - 25 IDcode idCode ID code of related entry. 27 – 30 IDcode idCode ID code of related entry. 32 - 35 IDcode idCode ID code of related entry. 37 - 40 IDcode idCode ID code of related entry. 42 - 45 IDcode idCode ID code of related entry. 47 - 50 IDcode idCode ID code of related entry. 52 - 55 IDcode idCode ID code of related entry. 57 - 60 IDcode idCode ID code of related entry. 62 - 65 IDcode idCode ID code of related entry. 67 - 70 IDcode idCode ID code of related entry. 72 - 75 IDcode idCode ID code of related entry. 77 - 80 IDcode idCode ID code of related entry.
Details
Verification/Validation/Value Authority Control
This record will be generated at the time of processing the component PDB files of the large macromolecular complex when all complex constituents are deposited.
Relationships to Other Record Types
REMARK 350 will contain an amended statement to reflect the entire complex.
Examples
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 SPLIT 1VOQ 1VOR 1VOS 1VOU 1VOV 1VOW 1VOX 1VOY 1VP0 1VOZ
Overview
CAVEAT warns of errors and unresolved issues in the 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 - 79 String comment Free text giving the reason for the CAVEAT.
Details
Verification/Validation/Value Authority Control
CAVEAT will be added to entries known to be incorrect.
Overview
The COMPND record describes the macromolecular contents of an entry. Some cases where the entry contains a standalone drug or inhibitor, the name of the non-polymeric molecule will appear in this record. 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, staff may exercise editorial judgment in consultation with depositors in assigning these names.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------------------- 1 - 6 Record name "COMPND" 8 - 10 Continuation continuation Allows concatenation of multiple records. 11 - 80 Specification compound Description of the molecular components. list
Details
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). 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 Indicates if there is a mutation. OTHER_DETAILS Additional comments.
Verification/Validation/Value Authority Control
CHAIN must match the chain identifiers(s) of the molecule(s). EC numbers are also checked.
Relationships to Other Record Types
In the case of mutations, the SEQADV records will present differences from the reference molecule. REMARK records may further describe the contents of the entry. Also see verification above.
Examples
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HEMOGLOBIN ALPHA CHAIN;
COMPND 3 CHAIN: A, C;
COMPND 4 SYNONYM: DEOXYHEMOGLOBIN ALPHA CHAIN;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: HEMOGLOBIN BETA CHAIN;
COMPND 9 CHAIN: B, D;
COMPND 10 SYNONYM: DEOXYHEMOGLOBIN BETA CHAIN;
COMPND 11 ENGINEERED: YES;
COMPND 12 MUTATION: YES
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: A;
COMPND 4 EC: 3.2.1.14, 3.2.1.17;
COMPND 5 OTHER_DETAILS: PLANT ENDOCHITINASE/LYSOZYME
Overview
The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry. Some cases where the entry contains a standalone drug or inhibitor, the source information of this molecule will appear in this record. 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" 8 - 10 Continuation continuation Allows concatenation of multiple records. 11 - 79 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. ORGANISM_TAXID NCBI Taxonomy ID number 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/outside the cell. PLASMID Identifies the plasmid containing the gene. GENE Identifies the gene. EXPRESSION_SYSTEM Scientific name of the organism in which the molecule was expressed. EXPRESSION_SYSTEM_COMMON Common name of the organism in which the molecule was expressed. EXPRESSION_SYSTEM_TAXID NCBI Taxonomy ID of the organism used as the expression system. 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.
- 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 third example below).
- 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.
Verification/Validation/Value Authority Control
The biological source is compared to that found in the sequence databases. The Tax ID is identified and the corresponding scientific and common names for the organism is matched to a standard taxonomy database (such as NCBI).
Relationships to Other Record Types
Each macromolecule listed in COMPND must have a corresponding source.
Examples
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: AVIAN SARCOMA VIRUS;
SOURCE 3 ORGANISM_TAXID: 11876
SOURCE 4 STRAIN: SCHMIDT-RUPPIN B;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PRC23IN
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
SOURCE 3 ORGANISM_COMMON: CHICKEN;
SOURCE 3 ORGANISM_TAXID: 9031
SOURCE 4 ORGAN: HEART;
SOURCE 5 TISSUE: MUSCLE
For a Chimera protein:
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: MOUSE, HUMAN; SOURCE 3 ORGANISM_TAXID: 10090, 9606 SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 344601 SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B171; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P4XH-M13;
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 - 79 List keywds Comma-separated list of keywords relevant to the entry.
Details
- Functional classification. - Metabolic role. - Known biological or chemical activity. - Structural classification.
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 by the wwPDB. 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 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
KEYWDS LYASE, TRICARBOXYLIC ACID CYCLE, MITOCHONDRION, OXIDATIVE
KEYWDS 2 METABOLISM
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:
X-RAY DIFFRACTION FIBER DIFFRACTION NEUTRON DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLID-STATE NMR SOLUTION NMR SOLUTION SCATTERING
*Note:Since October 15, 2006, theoretical models are no longer accepted for deposition. Any theoretical models deposited prior to this date are archived at https://files.wwpdb.org/pub/pdb/data/structures/models.
Please see the documentation from previous versions for the related file format description.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------------ 1 - 6 Record name "EXPDTA" 9 - 10 Continuation continuation Allows concatenation of multiple records. 11 - 79 SList technique The experimental technique(s) with optional comment describing the sample or experiment.
Details
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, as in the cases of NMR or electron microscopy studies, that the appropriate CRYST1 and SCALE values are used.
Relationships to Other Record Types
If the experiment is an NMR or electron microscopy 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.
Examples
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
EXPDTA X-RAY DIFFRACTION
EXPDTA NEUTRON DIFFRACTION; X-RAY DIFFRACTION
EXPDTA SOLUTION NMR
EXPDTA ELECTRON MICROSCOPY
Overview
The NUMMDL record indicates total number of models in a PDB entry.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------------ 1 - 6 Record name "NUMMDL" 11 - 14 Integer modelNumber Number of models.
Details
Verification/Validation/Value Authority Control
The verification program checks that the modelNumber field is correctly formatted.
Example
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
NUMMDL 20
Overview
The MDLTYP record contains additional annotation pertinent to the coordinates presented in the entry.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------------ 1 - 6 Record name "MDLTYP" 9 - 10 Continuation continuation Allows concatenation of multiple records. 11 - 80 SList comment Free Text providing additional structural annotation.
Details
Verification/Validation/Value Authority Control
The chain_identifiers described in this record must be present in the COMPND, SEQRES and the coordinate section of the entry.
Example
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MDLTYP MINIMIZED AVERAGE
MDLTYP CA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K ; P ATOMS ONLY,
MDLTYP 2 CHAIN X, Y, Z
MDLTYP MINIMIZED AVERAGE ; CA ATOMS ONLY, CHAIN A, B
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 - 79 List authorList List of the author names, separated by commas.
Details
- 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. - Umlauts and other character modifiers are not given.
- 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 Jr., II, or III - Abbreviations that are part of a surname, such as Jr., St. or Ste., are followed by a period and a space before the next part of the surname.
- 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.
- Line breaks between multiple lines in the authorList occur only after a comma. - Personal names are not split across two lines.
- Names are given in English if there is an accepted English version; otherwise in the native language, transliterated if necessary.
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
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
AUTHOR M.B.BERRY,B.MEADOR,T.BILDERBACK,P.LIANG,M.GLASER,
AUTHOR 2 G.N.PHILLIPS JR.,T.L.ST. STEVENS
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) in DD-MMM-YY format. This is
not repeated on continued lines.
24 - 27 IDCode modId ID code of this entry. This is not repeated on
continuation lines.
32 Integer modType An integer identifying the type of
modification. For all revisions, the
modification type is listed as 1
40 - 45 LString(6) record Modification detail.
47 - 52 LString(6) record Modification detail.
54 - 59 LString(6) record Modification detail.
61 - 66 LString(6) record Modification detail.
Details
0 Initial released entry. 1 Other modification.
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
In the case of a version revision, the current will be specified in REMARK 4.
Template
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12345678901234567890123456789012345678901234567890123456789012345678901234567890
REVDAT 2 15-OCT-99 1ABC 1 REMARK
REVDAT 1 09-JAN-89 1ABC 0
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REVDAT 2 11-MAR-08 2ABC 1 JRNL VERSN
REVDAT 1 09-DEC-03 2ABC 0
Overview
The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and removed from the PDB release set. One entry may replace many.
It is wwPDB policy that only the principal investigator of a structure has the authority to obsolete 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. 72 - 75 IDcode sIdCode ID code of a superseded entry.
Details
Verification/Validation/Value Authority Control
wwPDB checks that the superseded entries have actually been removed 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 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SPRSDE 17-JUL-84 4HHB 1HHB
SPRSDE 27-FEB-95 1GDJ 1LH4 2LH4
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.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ----------------------------------------------------------------------- 1 - 6 Record name "JRNL" 13 - 79 LString text See Details below.
Details
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 - 79 List authorList List of the authors.
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 - 79 LString title Title of the article.
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 - 79 LString title Title of the article.
4a. If the reference has not been published yet, 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"
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 PubMed with periods.
If the publication is a book, monograph, or other non-serial item, use its full name according to the Anglo-American Cataloguing Rules, 2nd Revised Edition; (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, verifiable 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 the 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. The series name should be listed in full unless the series has an accepted ISO abbreviation. 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 its number and/or letter in the series.
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.
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.
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".
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 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.
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.
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.
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)".
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.
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"
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" 36 - 39 LString(4) "ISSN" or International Standard Serial Number or "ESSN" Electronic Standard Serial Number. 41 - 65 LString issn ISSN number (final digit may be a letter and may contain one or more dashes).
COLUMNS DATA TYPE FIELD DEFINITION -------------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(4) "PMID" 20 – 79 Integer continuation unique PubMed identifier number assigned to the publication describing the experiment. Allows for a long PubMed ID number.
COLUMNS DATA TYPE FIELD DEFINITION -------------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(4) "DOI " 20 – 79 LString continuation Unique DOI assigned to the publication describing the experiment. Allows for a long DOI string.
Verification/Validation/Value Authority Control
wwPDB verifies that this record is correctly formatted.
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 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
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 ISSN 0022-2836
JRNL PMID 6726807
JRNL DOI 10.1016/0022-2836(84)90472-8
Known Problems