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

Summer 2009
Number 42

 
NEWSLETTER
  Contents  
Home | Newsletter Archive | PDF Version
Message from the RCSB PDB
Data Deposition
5 Easy Steps for Structure Deposition
Improve the Quality of Your Depositions with SFCHECK
How does an HPUB structure get released?
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
Literature View: Looking at Structures in PubMedCentral
Customizable Structure Summary Pages
MyPDB: Keep up-to-date with new structures... automatically!
Ligand Expo: Searching and Browsing Features
Outreach and Education
Recent and Upcoming Meetings and Presentations
Congratulations to National Tournament Champions
wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe
Looking at Structures: A Resource for Learning About PDB Data
Education Corner
Community Outreach
PDB Community Focus
Gregory Warren, OpenEye Scientific Software, Inc.
RCSB PDB PARTNERS, MANAGEMENT, AND STATEMENT OF SUPPORT
 
     

DATA DEPOSITION

5 Easy Steps for Structure Deposition



These steps, along with a checklist of items needed for deposition, are described in an updated brochure called 5 Easy Steps for Structure Deposition. For a printed copy or for a packet of information about the deposition process, please send your postal address to info@rcsb.org.
Depositors can follow these steps to make the process of depositing a structure quick, easy, and accurate!

1. Check the sequence, which should contain all residues used in the experiment, including expression tags and residues missing due to disorder. Use BLAST1 to determine the appropriate sequence database references for the proteins or nucleic acids present in the file. Any sequence mismatches should correspond to mutation, variant or expression tags in the submitted sequence.

2. Check the ligands. Ligand Expo can be used to see if any of the chemical components in the structure (ligands, drugs, inhibitors, ions, modified residues, etc.) already exist in the Chemical Component Dictionary. If found, use the corresponding 3-character code in the coordinates; otherwise, the new component can be uploaded in ADIT along with the structure.

3. Prepare data for deposition. Use pdb_extract to automatically collect information needed for deposition from the output files produced by many structure determination applications, and SF-Tool to convert the structure factor file format and check the data with SFCHECK.2

4. Validate the structure with the Validation Suite and Server to ensure that the data being deposited are accurate and reflect what you intend to submit. This program checks the sequence and file format consistency, compares geometrical and chemical interactions to various standards, and reports errors that should be corrected before deposition.

5. Deposit using ADIT/ADIT-NMR to check, validate, and edit the PDB data entries. Deposition is an iterative process. If you encounter problems at any particular step, please make the correction(s) and go through the steps again. For more information, please see deposit.pdb.org.



Improve the Quality of Your Depositions with SFCHECK

SFCHECK2 is integrated with the RCSB PDB's deposition tools so users can assess the agreement between an atomic model and the corresponding X-ray data before a structure is deposited and released.

SFCHECK generates reports containing R-factors, density correlation, Luzzati plots, Wilson plots, temperature factors, local error estimation by residues, and more. It is a part of the Validation Server and ADIT tools, and is used by the RCSB PDB during the annotation process.

SFCHECK is also part of SF-Tool, a streamlined, web-based tool for validating crystallographic experimental data. In addition to validating model coordinates against structure factor data with SFCHECK, SF-Tool can:

  • Easily translate a structure factor file between different formats (mmCIF, CIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, XSCALE, D*Trek, SAINT, other)
  • Check for twinned or detwinned data Depositors are strongly encouraged to use SFCHECK before deposition.

For more information, please see deposit.pdb.org.


How does an HPUB structure get released?

An HPUB status indicates that a structure will be released when the primary reference is published (?hold until publication?). Once it is confirmed that the corresponding article is available, the structure is released in the weekly update of the PDB.

The wwPDB receives publication dates and citation information directly from a few journals. For most articles, however, the wwPDB searches PubMed and scans the literature for publication information. Citations emailed to deposit@wwpdb.org are also greatly appreciated.

There is a one-year limit on the length of a hold period, including those for HPUBs. If the citation for a structure is not published within the one-year period, depositors will be given the option to either release or withdraw the deposition.


Deposition Statistics

In the second quarter of 2009, 2079 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, 72.7% were deposited with a release status of HPUB; 24.6% were released as soon as annotation of the entry was complete; and 2.7% were held until a particular date. 91.8% of these entries were determined by X-ray crystallographic methods; 7.3% were determined by NMR methods.

1874 structures were released in the PDB during the same period.


1 S.F. Altschul, W. Gish, W. Miller, E.W. Myers, & D.J. Lipman (1990) Basic local alignment search tool. J. Mol. Biol. 215:403-410.

2 A.A. Vaguine, J. Richelle, S.J. Wodak (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr. D55:191-205.

 
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