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wwPDB Announcement: Deposition and Release of PDB Entries Containing Large Structures

In order to meet the challenges of ever greater numbers of PDB depositions, involving ever larger and more complex structures, often determined using multiple methods, the Worldwide Protein Data Bank partners (wwPDB; http://wwpdb.org/) are developing a completely new system for deposition and annotation of PDB entries. This new system will go into full production at all the wwPDB deposition sites early in 2014 and will then be able to handle depositions of structures of any size, determined using diffraction, NMR and/or EM methods. Large structures will also be processed and released intact so that "split entries" become a thing of the past.

Currently, submitting a large structure that exceeds PDB format restrictions (e.g., more than 62 chains or more than 99,999 atoms) requires the depositor to split the large structure into multiple PDB files. The new wwPDB deposition and annotation system will be able to handle such structures if they are provided in a single file in PDBx/mmCIF format. The PDBx/mmCIF (http://mmcif.pdb.org/) format does not suffer the restrictions of the PDB format and is capable of representing large structures in a single file.

With the new deposition system, large structures that are deposited as a single PDBx/mmCIF file will also be processed and released into the PDB ftp archive as a single PDBx/mmCIF file (along with a companion PDBML format file). Since the coordinate records in such structures cannot be validly represented by the PDB format, only an abbreviated PDB formatted file, containing authorship and citation details, will be provided in the ftp archive. In addition, a web service will be provided by the wwPDB to translate the coordinate records and limited metadata into a collection of limited, "best-effort" PDB-format files. (Structures that do not exceed the limitations of the PDB format will continue to be provided as PDB files in the archive for the foreseeable future.)

The wwPDB has convened a Working Group for PDBx/mmCIF Data Deposition (http://wwpdb.org/workshop/wgroup.html) that includes representatives from the major X-ray structure-determination packages, and is chaired by Paul Adams. In order to ease the transition from PDB to PDBx/mmCIF, the Working Group has made recommendations about essential extensions required for large structures, including:

  • Atom serial numbers will run from 1 to the number of deposited atoms (with no field-width restrictions);
  • Chain identifiers of up to 4 characters will be allowed;
  • Cartesian coordinates will have field width as large as required (and maintain 3 decimal places precision);
  • Isotropic B-factors and occupancies will have 3 decimal places precision.

PDBx/mmCIF files suitable for deposition can now be created with recent versions of the CCP4 (REFMAC 5.8) and Phenix (1.8.2) software packages. Both packages support the above extensions for large structures.

Although the new wwPDB deposition and annotation system will not go into full production until early 2014, limited external testing will commence in August 2013. We invite depositors of large structures (that currently break the PDB format restrictions and necessitate splitting of entries) to contact info@wwpdb.org to gain access to the new system as beta testers.

Prior to the release of the new deposition system in 2014, depositors needing to submit large entries as a single PDBx/mmCIF data file should contact info@wwpdb.org. The wwPDB will arrange to accept and process the large entries intact and provide a special download location on the wwPDB ftp site for the large entry (ftp://ftp.wwpdb.org/pub/pdb/data/large_structures). In order not to break any current software systems, wwPDB curators will "split" such an entry into a collection of PDB-format files that will be distributed on the wwPDB ftp site following current release and formatting conventions. In 2014, all legacy split entries will be "reunited" and released intact (in PDBx/mmCIF format only) by the wwPDB.

Users with questions about the new deposition system or the procedures for handling large structures should contact info@wwpdb.org.

source: wwpdb.org news/22-May-2013