Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Winter 2013
Number 56


Data Deposition and Annotation

 The first high-resolution 3D structure of a DNA origami object from nanotechnology is also the first PDB structure that contains an entire genome. PDB entries (2YMF, 2YMG, 2YMH, 2YMI and 2YMR)

2012 Deposition Statistics

In the fourth quarter of 2012, 2385 experimentally-determined structures were deposited to the PDB archive for a total of 9964 entries deposited in the year. 9250 entries were deposited in 2011.

Of all structures deposited in 2012, 81.5% were deposited with a release status of hold until publication; 14.5% were released as soon as annotation of the entry was complete; and 4.0% were held until a particular date. 93.0% of these entries were determined by X-ray crystallographic methods; 5.9% were determined by NMR methods.

8978 structures were released in the PDB archive in 2012. They account for ~10% of the current total holdings of 87153.

wwPDB News

New Reference Dictionary for Biologically Interesting Molecules Released

The wwPDB has reviewed the representation of peptide-like antibiotic and inhibitor molecules in the PDB archive. As a result, a new reference dictionary has been created to help define and represent these biologically interesting molecules.

This Biologically Interesting molecule Reference Dictionary (BIRD) contains chemical descriptions, sequence and linkage information, and functional and classification information as taken from the core structures and from external resources. PDB entries containing these molecules have been annotated using this dictionary, and will contain a corresponding BIRD ID code only in the PDBx-formatted file.

BIRD is available on the wwPDB FTP server adjacent to the Chemical Component Dictionary. The use of BIRD will greatly improve the consistency of peptide-like antibiotic and inhibitor molecules in the PDB.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.

Remediation of Structure Factor Data and Release Plan

The wwPDB has reviewed structure factor files in the archive for format consistency and correspondence with coordinate data. As a result, around 43,800 structure factor files have been updated to standardize the format and to incorporate data corrections. Changes made are described in the audit.details record of the structure factor file.

Starting January 16, 2013, the wwPDB will begin to release these modified structure factors in weekly batches of 1000. These files will be available from ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/structure_factors/.

Experimental Data Release Policy Clarification

Effective February 6, 2013, coordinates and experimental data deposited in the PDB will follow the same release status.