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

Fall 2009
Number 43

 
NEWSLETTER
  Contents  
Home | Newsletter Archive | PDF Version
Message from the RCSB PDB
Data Deposition
SF-Tool: A Tool for Crystallographic Experimental Data Validation
Meeting with Depositors at the ACA
Deposition Statistics
Structural Genomics News
Data Query, Reporting and Access
Improved Navigation of the RCSB PDB Website
Sequence Similarity Views of PDB Structures
New Tool For Exploring Sequence and Structure Alignments
Beta Release of Redesigned BioSync
wwPDB FTP Advisory Notice
Outreach and Education
Poster Prizes Awarded at ACA and ISMB
Recent and Upcoming Meetings and Presentations
Turn Your Computer into a PDB Structure Kiosk
Education Corner
Gary M. Battle, Ph.D.: Symposium on the Applications of Small-molecule Crystal Structure Information in Chemical Education
PDB Community Focus
Roland L. Dunbrack, Jr., Ph.D., Fox Chase Cancer Center
RCSB PDB PARTNERS, MANAGEMENT, AND STATEMENT OF SUPPORT
 
     

DATA DEPOSITION

SF-Tool: A Tool for Crystallographic Experimental Data Validation

A streamlined, web-based tool can validate crystallographic experimental data. SF-Tool can be used to:

  • Validate model coordinates against structure factor data (using SFCheck)1
  • Easily translate your structure factor file between different formats (mmCIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, D*Trek, SAINT, or OTHER format)
  • Check for twinned or detwinned data

SF-Tool can be accessed along with other programs for data validation and deposition at deposit.pdb.org. Questions, comments, and suggestions should be sent to help@deposit.pdb.org.


Meeting with Depositors at the ACA

The RCSB PDB exhibited alongside the PSI Structural Genomics Knowledgebase (PSI SGKB) at the 2009 Meeting of the American Crystallographic Association (July 25-30; Toronto, Canada). Many data depositors and users visited the booth for the latest RCSB PDB publications, to ask questions, and to give feedback on new website features.

The scientific poster "The PDB: Updates and Future Plans" highlighted the recent improvements made to the PDB File Format and future plans for a common wwPDB deposition and annotation tool.

As part of the Crystallography Education session, a presentation on Looking at Structures with Diverse Audiences was given.

 
Many visitors came to the RCSB PDB stand for materials, demonstrations, and to talk to team members.
The ACA exhibition hall saw the debut of the new poster How Do Drugs Work? This poster, which highlights several protein-drug PDB structures, will be distributed at the RCSB PDB booth at several upcoming meetings.

Deposition Statistics

In the third quarter of 2009, 2085 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, 74.8% were deposited with a release status of HPUB; 22.6% were released as soon as annotation of the entry was complete; and 2.6% were held until a particular date. 93.0% of these entries were determined by X-ray crystallographic methods; 6.2% were determined by NMR methods.

1927 structures were released in the PDB during the same period.


Structural Genomics News

Two structural genomics centers recently made the news for reaching deposition milestones this summer.

In July, the Midwest Center for Structural Genomics (MCSG; www.mcsg.anl.gov) became the first Protein Structure Initiative (PSI) center to determine its 1,000th protein structure. Founded in 2000, the MCSG targets proteins from several biomedical and special classes, with a particular focus on characterization of potential novel virulence factors, pathogenic factors, and cases of viral molecular mimicry in pathogenic bacteria uncovered by bioinformatics methods as part of the NIH-funded PSI efforts.



The MCSG?s 1,000th protein structure is a dehydrogenase from the bacterium Colwellia psychrerythraea. The enzyme is capable of generating harmful reactive oxygen species and has been implicated in neurodegeneration, ischemia-reperfusion, cancer and several other disorders. PDB ID: 3ic9, DOI:10.2210/pdb3ic9/pdb

In August, investigators at the Center for Structural Genomics of Infectious Diseases (CSGID; csgid.org/csgid) determined their 100th pathogen protein structure in less than two years. Funded by the National Institute of Allergy and Infectious Diseases, the CSGID applies structural genomics approaches to potential drug targets from NIAID category A, B, and C priority pathogens, with the goal of solving 500 structures over a five-year period.



The 100th protein structure is a BA2930 protein thought to be a major part of anthrax's resistance mechanism to the aminoglycoside family of antibiotics, including streptomycin, gentamycin and kanamycin.
PDB ID: 3ijw, DOI:10.2210/pdb3ijw/pdb


Current structural genomics news, features, and highlights are available from the PSI Structural Genomics Knowledgebase at kb.psi-structuralgenomics.org.


1. 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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