International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.6, pp. 191-193

Section 3.6.8.3. Citation of related database entries

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.8.3. Citation of related database entries

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Categories describing related database entries are as follows:

DATABASE group
Related database entries (§3.6.8.3.1[link])
 DATABASE
 DATABASE_2
Compatibility with PDB format files (§3.6.8.3.2[link])
 DATABASE_PDB_CAVEAT
 DATABASE_PDB_MATRIX
 DATABASE_PDB_REMARK
 DATABASE_PDB_REV
 DATABASE_PDB_REV_RECORD
 DATABASE_PDB_TVECT

The purpose of entries in the DATABASE category group is to provide pointers that link the mmCIF to all database entries that result from the deposition of the file. For mmCIF, the relevant category is DATABASE_2, which replaces the DATABASE category of the core dictionary.

Note the distinction between the database pointers provided here and those in the STRUCT_REF family of categories. The latter are intended to provide links to external database entries for any aspect of any subset of the structure that the author may wish to record, including previous determinations of the same structure, other structures containing the same ligand or references to the sequence(s) of the macromolecule(s) in sequence databases. In contrast, the links provided in DATABASE_2 refer to the entire contents of the mmCIF and are designed to cover situations in which the entire file is deposited in more than one database (for example, in the PDB and in a database for protein kinases).

3.6.8.3.1. Related database entries

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Data items in these categories are as follows:

(a) DATABASE [Scheme scheme191]

(b) DATABASE_2 [Scheme scheme192]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ([\rightarrow]) is a reference to a parent data item. Items in italics have aliases in the core CIF dictionary formed by changing the full stop (.) to an underscore (_).

The DATABASE category is retained in the mmCIF dictionary, but only for consistency with the core dictionary.

The role of the data items in the DATABASE_2 category is to store identifiers assigned by one or more databases to the structure described in the mmCIF. In the data model used in the core CIF dictionary, each database has an individual data item. The data model in mmCIF is more general. It comprises the data items _database_2.database_id, which identifies the database, and _database_2.database_code, which is the code assigned by the database to the entry. Thus a new database can be referred to without needing to add an additional data item to the dictionary. If a structure has been deposited in more than one database, the values of _database_2.database_id and _database_2.database_code can be looped.

The institutions and individual databases recognized in the DATABASE_2 category in the current version of the mmCIF dictionary are CAS (Chemical Abstracts Service), CSD (Cambridge Structural Database), ICSD (Inorganic Crystal Structure Database), MDF (Metals Data File), NDB (Nucleic Acid Database), NBS (the Crystal Data database of the National Institute of Standards and Technology, formerly the National Bureau of Standards), PDB (Protein Data Bank), PDF (Powder Diffraction File), RCSB (Research Collaboratory for Structural Bioinformatics) and EBI (European Bioinformatics Institute). It is intended that new databases will be added to this list on an ongoing basis; the purpose of specifying a list of possible databases in the dictionary is to ensure that each database is referenced consistently.

3.6.8.3.2. Compatibility with PDB format files

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Data items in these categories are as follows:

(a) DATABASE_PDB_REV [Scheme scheme193]

(b) DATABASE_PDB_REV_RECORD [Scheme scheme194]

(c) DATABASE_PDB_MATRIX [Scheme scheme195]

(d) DATABASE_PDB_TVECT [Scheme scheme196]

(e) DATABASE_PDB_CAVEAT [Scheme scheme197]

(f) DATABASE_PDB_REMARK [Scheme scheme198]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ([\rightarrow]) is a reference to a parent data item.

A major goal of the design of the mmCIF data model was that a file could be transformed from Protein Data Bank (PDB) format to mmCIF format and back again without loss of information. This required the creation of mmCIF data items whose sole purpose is to capture PDB-specific records that do not map onto mmCIF data items. These records would never be created for a de novo mmCIF. This family of categories also belongs to the PDB category group (see Section 3.6.9.3[link]).

The items in the categories DATABASE_PDB_MATRIX and DATABASE_PDB_TVECT are derived from the elements of transformation matrices and vectors used by the Protein Data Bank. The items in the categories DATABASE_PDB_REV and DATABASE_PDB_REV_RECORD record details about the revision history of the data block as archived by the Protein Data Bank.

The items in the DATABASE_PDB_CAVEAT category record comments about the data block flagged as `CAVEATS' by the Protein Data Bank at the time the original PDB archive file was created. A PDB CAVEAT record indicates that the entry contains severe errors. In PDB format, extended comments were stored as a sequence of fixed-length (80-character) format records, columns 9 and 10 being reserved for continuation sequence numbering. The mmCIF representation retains each record as a separate data value and does not attempt to merge continuation records to provide more readable running text. Hence the PDB CAVEAT entry [Scheme scheme199] would be represented in mmCIF as [Scheme scheme200]

The PDB format used `REMARK' records to store information relating to several aspects of the structure in free or loosely structured text. In some cases, the conventions used for individual types of REMARK record allow structured data to be extracted automatically and translated to specific mmCIF data items. Where this is not possible, the DATABASE_PDB_REMARK category may be used to retain the information that appeared in these parts of PDB format files. Unlike the CAVEAT records, it is possible to collect together several REMARK records sharing a common numbering into a single free-text field. For example, PDB practice has been to repeat the contents of CAVEAT records (see above) as records of type `REMARK 5'. While each separate CAVEAT record is converted to a separate mmCIF data value, the complete text of a REMARK 5 record may be gathered into a single mmCIF data value. Hence the CAVEAT example above would also appear in a PDB file as part of a `REMARK 5' as [Scheme scheme201] and would appear in an mmCIF as [Scheme scheme202]

Note that by convention the value of _database_PDB_remark.id matches the class of the REMARK record in the PDB file.








































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