DATA DEPOSITION AND PROCESSING

WEEKLY DEADLINES FOR RELEASE/MODIFY ENTRY REQUESTS

P
DB entries are processed by the three members of the wwPDB (RCSB, MSD-EBI and PDBj), and are released immediately (REL), when the corresponding paper is published (HPUB), or on a particular date (HOLD).

Each week, all files scheduled for release or modification are checked and validated one final time. Authors may be contacted to resolve any issues that may arise while preparing the entries for release.

When the release of HPUB structures is requested, the PDB staff routinely confirms the primary citation. If this is not accomplished within that release cycle, the entry may be scheduled to be released in a later update.

To be included in the next update, any required author correspondence should be sent to the appropriate wwPDB member by the following times:

All entries due for release are transferred to the RCSB for final packaging into the master PDB ftp archive. These files are then released by 4:00 EST each Wednesday.

Requests received after these cutoff times will be processed during the next update cycle.

CHANGES AND CORRECTIONS TO ENTRIES IN THE PDB ARCHIVE

C
orrections to entries originally processed by the RCSB, EBI-MSD, or PDBj are handled by the same annotation staff and subsequently reviewed by the author(s) depositing the structure. Any changes in released PDB entries are described in the PDB REVDAT records and in the mmCIF/XML DATABASE_PDB_REV_RECORD category.

When replacement coordinates for a released entry are provided by the depositing author, the original entry is obsoleted and the replacement coordinates are released in a new superseding PDB entry. The relationship between obsolete and superseding entries is stored in OBSLTE/SPRSDE PDB records and in the mmCIF/XML category PDBX_DATABASE_PDB_OBS_SPR. Queries of obsoleted entries on the RCSB PDB website always produce the most recent superseding entry. Obsoleted entries remain available in a separate area of the PDB ftp site, ftp://ftp.rcsb.org/pub/pdb/data/structures/obsolete/.

For the entries deposited prior to 1998, a variety of consistency checks have been performed. This has been done as part of an ongoing wwPDB project to maintain uniformity within the PDB archive. Examples of uniformity corrections include corrections related to atomic nomenclature for both macromolecule(s) and ligand(s), sequence-coordinate consistency, and the addition of missing records (e.g. citations, synonyms, and sequence database references). Data uniformity efforts by MSD-EBI and PDBj will be incorporated into these data in the near future.

Corrections in the pre-1998 entries have been made only in the mmCIF and XML data files. The mmCIF and XML data files are offered as download options on the RCSB PDB website and are also available via ftp.

The XML data files were produced as part of a joint project by all wwPDB members, and these files are in the final stage of beta testing. Both mmCIF and XML data files conform to the PDB Exchange data dictionary. This dictionary is available in both mmCIF and XML schema form at http://deposit.pdb.org/mmcif/.

PDB DEPOSITION STATISTICS

I
n the first quarter of 2005, 1398 experimentally-determined structures were deposited to the PDB archive.

The entries were processed by wwPDB team members at RCSB-Rutgers, MSD-EBI, and PDBj. Of the structures deposited, 71% were deposited with a release status of HPUB; 18% were REL; and 11% with HOLD.

84% of these entries were determined by X-ray crystallography; 14% were determined by NMR. 82% were deposited with experimental data. 57% released the sequence in advance of the structure's release.