Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank

Winter 2009
Number 40

Home | Newsletter Archive | PDF Version | Text-only Version
Message from the RCSB PDB
Data Deposition
PDB Archive Version 3.15 to be Released
Tips for Depositing Multiple Related Structures using ADIT/ADIT-NMR
2008 Deposition Statistics
Data Query, Reporting and Access
2008 Website Statistics
View Domain Annotations in 3D
Getting Started with the RCSB PDB Website
Browser Check for Compatibility with Website Features
Outreach and Education
Meetings and Presentations
Looking at Structures: A Resource for Learning About PDB Data
Publications: 2008 Annual Report and more
Education Corner
Bernadette Uzzi, Coordinator, The Science Learning Center at Brookhaven National Laboratory
PDB Community Focus
Johannes Kirchmair, Ph.D., and Gerhard Wolber, Ph.D., University of Innsbruck


PDB Archive Version 3.15 to be Released

A new standardized version of the PDB archive will be available from in early 2009. The date will be announced at

As of December 2, 2008, all new PDB releases follow PDB File Format Contents Guide Version 3.20. With the new version of the archive, all entries released prior to December 2, 2008 will be re-released as PDB Format Version 3.15 files. This release will overwrite all existing files.

A snapshot of the archive before this release will be available from Tools for downloading the archive can be found at For file format documentation, please see

Questions may be sent to

Tips for Depositing Multiple Related Structures using ADIT/ADIT-NMR

For depositing many structures that are related to one another, there are a few ways of making the ADIT/ADIT-NMR deposition process simpler:

  • Use pdb_extract when preparing structures solved using X-ray crystallography or NMR. Not only does pdb_extract minimize the amount of manual typing needed during the deposition process, it also utilizes an author information form that can be filled out just one time for use with multiple entries.

    pdb_extract takes information about data collection, phasing, density modification, and the final structure refinement from the output files and log files produced by the various applications used for structure determination. The collected information is organized into a file ready for deposition using ADIT/ADIT-NMR.

    The author information form in pdb_extract contains author names, citation information, protein names and source–the types of information that are repeated in multiple related entries. This form can be filled out once and used with pdb_extract to prepare several structures for deposition.

  • For structures solved by other experimental methods, first deposit one representative structure. After it has been annotated and processed, use this finalized entry as a template for the related depositions by replacing the coordinates and updating information in the PDB or mmCIF file as necessary.

  • If the structures have bound ligands, drugs, or inhibitors, please check Ligand Expo for matching chemical components. If a match is found, use that corresponding ID code for the component in your coordinates. If a match is not found, choose a new three-character code for the component, and upload the chemical name and a file showing the chemical drawing for the new component into the Ligand Information section of ADIT/ADIT-NMR.

These resources and more can be found at

2008 Deposition Statistics

In 2008, 7043 experimentally-determined structures were deposited to the PDB archive.

The entries were processed by wwPDB teams at the RCSB PDB, PDBe, and PDBj. Of the structures deposited in 2008, 75.7% were deposited with a release status of "hold until publication"; 19.5% were released as soon as annotation of the entry was complete; and 4.8% were held until a particular date.

90.9 % of these entries were determined by X-ray crystallographic methods; 8.1% were determined by NMR methods. Since February 1, 2008, depositing structure factor amplitudes/intensities (for crystal structures) and restraints (for NMR structures) has been a mandatory requirement for PDB deposition. As a result, 98.7 % of the 2008 depositions were deposited with experimental data.

Also in 2008, 7072 structures were released into the archive.

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