Announcement: Comprehensive Format Guide
During the past year, wwPDB annotators have collaborated on a project to clarify the details and procedures related to data processing and annotation. The result is a PDB Contents Guide Version 3.2 that more fully describes the PDB file format. This document is available either as a PDF or via HTML from the wwPDB website, and is accompanied by a document highlighting these clarifications.
In the coming months, all files released by the wwPDB will follow the format as described in this document. Details will be made available at www.pdb.org and at www.wwpdb.org.
Ligand Expo: A Resource for Depositing Structures
The Chemical Component Dictionary archives chemical and structural information about all residue and small molecule components found in PDB entries. Ligand Expo is a tool that can access, visualize, and build reports about these data. It can also be used to prepare a file for deposition through the following process:
- Search Ligand Expo for a chemical component that matches your ligand
- If a match is found, use that corresponding three-letter code for the ligand in your coordinates
- If the ligand is not found, choose a new three-letter code for the ligand
- When depositing your structure with ADIT, upload the chemical name and a file showing the chemical image for the new ligand into the Ligand Information section
Ligand Expo (ligand-expo.rcsb.org) is an update of the Ligand Depota resource.
PDB Focus: What is the Smallest Polymer Structure That Can Be Deposited to the PDB?
The PDB contains biomolecular polymers including polypeptides, polynucleotides, polysaccharides, and their complexes.
Polypeptide structures containing 24 or more residues can be deposited to the PDB. Smaller peptides that are complexed with a larger polymer (greater than the minimum length defined above) may be deposited to the PDB. Crystal structures of peptides with fewer than 24 residues, such as antibiotics, should be sent to the Cambridge Crystallographic Data Centre (CCDC; www.ccdc.cam.ac.uk).
Polynucleotide structures with 4 or more residues are accepted at the PDB. Smaller oligonucleotides (dinucleotides and trinucleotides) can be deposited at the Nucleic Acid Database (NDB; ndbserver.rutgers.edu).
Coordinates for the repeating unit of fibrous polymers and polysaccharide structures with 4 or more sugar residues may be deposited at the PDB archive. Molecules that do not conform to these guidelines but have been previously deposited in the archive will not be removed.
Structures may be deposited to the archive via the wwPDB.
ADIT Focus: Restarting Deposit Sessions
A structure can be deposited over a period of time by using ADIT's "Session Restart ID" feature. This identifier appears in red in the center of the browser window when ADIT's "deposit" step is first started. It is also seen in the title of the browser throughout the deposition session.
The case-sensitive restart ID should be entered in the space provided on the ADIT home page to return to the deposition session. Any data entered in a category are stored every time the user selects the SAVE button. All entered data associated with a particular entry can be accessed using the restart ID until the "DEPOSIT NOW" button is selected, for up to six months after the session has been last updated.
ADIT is available at the RCSB PDB and PDBj. ADIT-NMR can be used to deposit data to both the PDB and BMRB.
A tutorial guide to using ADIT is available in English and Japanese. Simulation sessions for "in progress" deposition are available to practice learning how to use ADIT at rcsb-deposit-demo-1.rutgers.edu.
In the third quarter of 2008, 1924 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, 76.9% were deposited with a release status of "hold until publication"; 18.1% were released as soon as annotation of the entry was complete; and 5.0% were held until a particular date. 92.2% of these entries were determined by X-ray crystallographic methods; 6.8% were determined by NMR methods.
During the same time period, 1928 structures were released in the PDB.
aZ. Feng, L. Chen, H. Maddula, O. Akcan, R. Oughtred, H.M. Berman, J. Westbrook (2004) Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 20:2153-2155.