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The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data.1 Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). The wwPDB's mission is to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community.

10-December-2014

Integration of Large Structures with the Main PDB Archive

With this week's update, large structures (containing >62 chains and/or 99999 ATOM lines) represented as single files have been fully integrated into the main PDB FTP archive in both PDBx/mmCIF and PDBML formats, as announced in September. Previously, large structures were represented in multiple "SPLIT" entries, which have now been removed (obsoleted). Users searching for ID codes of "SPLIT" entries at wwPDB member websites will be automatically redirected to the combined entry.

A separate directory in the PDB FTP archive contains a TAR file including a collection of "best-effort," minimal, PDB format files for large structures that contain authorship, citation details and coordinate data, and an index file that contains the mapping between the chains present in the large entry and the chains present in the limited PDB-format files. DOIs for large structures will point to these TAR files.

Large structures will only be distributed in the main PDB FTP directory in PDBx/mmCIF and PDBML formats, including biological assembly 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.

A snapshot of the FTP archive before this change is available at RCSB PDB and PDBj.

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1. H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980

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