FIVE EASY STEPS FOR FAST AND ACCURATE DATA DEPOSITION
1. Use PDB_EXTRACT 2. Validate your entry 3. Run BLAST 4. Use Ligand Depot 5. Deposit with ADIT
PDB ID: 1eul. Toyoshima, C., Nakasako, M., Nomura, H., Ogawa, H.: Crystal Structure of the Calcium Pump of Sarcoplasmic Reticulum at 2.6 Å Resolution. Nature 405 pp. 647 (2000)
ON THE COVER: PDB ID: 1lnx. Mura, C., Kozhukhovsky, A., Gingery, M., Phillips, M., Eisenberg, D.: The Oligomerization and Ligand-Binding Properties of Sm-Like Archaeal Proteins (Smaps) Protein Sci. 12 pp. 832 (2003)
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www.pdb.org • info@rcsb.org
AFTER DEPOSITION
The PDB ID assigned to the structure appears in the Web browser after successful deposition with the Web-based ADIT. For depositions sent via email or ftp, the PDB ID is returned by email, usually within 24 hours. Structures are typically processed, returned to the author for review, and finalized within 2 weeks of deposition.
WEBSERVER LOCATIONS
PDB_EXTRACT Validation Suite BLAST (from NCBI) Ligand Depot ADIT pdb-extract.rutgers.edu deposit.pdb.org/validate www.ncbi.nih.gov/BLAST ligand-depot.rutgers.edu deposit.pdb.org/adit (Rutgers-US) pdbdep.protein.osaka-u.ac.jp/adit (Osaka University, Japan)
RELEASE INFORMATION COORDINATE RELEASE:
Entries can be released immediately after processing (REL), held until publication (HPUB), or held until 6 months or 1 year after deposition (HOLD). There is a one-year limit on the length of a hold period, including hold for publication structures. If the citation for a structure is not published within the one-year period, depositors are given the option to either release or withdraw the deposition. Citation information should be sent to deposit@rcsb.rutgers.edu.
Crystal Structure Deposition Information
SEQUENCE RELEASE:
The sequence can be released ahead of the structure. Sequence data are available before the release of the corresponding coordinate data through the PDB status search at www.rcsb.org/pdb/status.html.
SOFTWARE DOWNLOADS
PDB_EXTRACT Validation Suite ADIT deposit.pdb.org/software/PDB_EXTRACT http://www.ccp4.ac.uk/ (CCP4i version 5.0) deposit.pdb.org/software/VAL deposit.pdb.org/software/ADIT
CITATION UPDATES:
Citations for structures are sent by depositors, users, selected journals, and by searching PubMed. Depositors are notified when a citation is found for structures on HPUB.
Validate structures and prepare depositions efficiently on your desktop and the Web using tools from the RCSB. PDB_EXTRACT, Ligand Depot, the PDB Validation Suite, and ADIT are tools that make checking and preparing structures for deposition fast and efficient. Software tools are available in source and binary form from deposit.pdb.org/software.
The RCSB Protein Data Bank (PDB) is operated by Rutgers, The State University of New Jersey; the San Diego Supercomputer Center at the University of California, San Diego; and the Center for Advanced Research in Biotechnology/UMBI/NIST—three members of the Research Collaboratory for Structural Bioinformatics (RCSB).
REFERENCES 1 Feng Z, Westbrook J, Berman HM. NUCheck: Rutgers University, New Brunswick, NJ; 1998. Report No.: NDB-407. 2 Laskowski RA, McArthur MW, Moss DS, et al. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 1993;26:283-291. 3 Vaguine AA, Richelle J, Wodak SJ. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr. 1999;D55:191-205. 4 Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) “Basic local alignment search tool.” J. Mol. Biol. 215:403-410.
PDB ID: 2hhb
Fermi, G., Perutz, M. F., Shaanan, B., Fourme, R.: The crystal structure of human deoxyhaemoglobin at 1.74 Å resolution. J Mol Biol 175 pp. 159 (1984)
QUESTIONS?
Deposition: deposit@rcsb.rutgers.edu Software installation: sw-help@rcsb.rutgers.edu
he RCSB Protein Data Bank has developed a variety of tools to facilitate data deposition and validation by the authors of structures, including PDB_Extract, ADIT, the Validation Suite, and Ligand Depot.
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3. RUN BLAST (FROM NCBI)
Input the complete deposition sequence (including residues not seen due to lack of electron density) into BLAST4 to compare your sequence to sequence database references. Any necessary corrections should then be made to your coordinates.
X-RAY STRUCTURE DEPOSITION CHECKLIST
o Contact authors name (including PI), e-mail address, postal address, phone and fax numbers o Title for the deposited structure and any relevant keywords o Citation information: author names, title, and journal details if these are available o Macromolecule and ligand names o Sequence and chain ID for each macromolecule, including his tags or cloning artifacts that were not cleaved and any residues not visible due to disorder o Source information: scientific names for source organisms, expression systems, or details about synthetically produced molecules o Biological assembly description o Crystallization details: method, pH, temperature, crystallization solution components o Cell dimensions and space group o Data collection information: type of diffraction experiment, radiation source, wavelength(s) used, detector type, collection temperature, number of crystals, and collection date o Data processing information: • High and low resolution limits • Percent of possible reflections observed • Observed criterion sigma (F) or observed criterion sigma (I) • Number of unique measured reflections (all and observed) • R-merge or R-sym for (I) observed • Details about the highest resolution shell o Refinement statistics: • Low and high resolution limits for data used in refinement • Structure determination method • Number of unique reflections (all and observed) used in refinement • Cut-off on sigma(F) • Cross-validation reflection selection details • Stereochemistry target values • At least one of the following: R-factor for all reflections, R-factor for reflections classified as observed, or R-factor for working set reflections and associated R-free for the cross-validation set o Software used for: data collection, data reduction, structure solution, and refinement o Structure factor file
1. USE THE PDB_EXTRACT PROGRAM SUITE
PDB_EXTRACT contains tools and examples for extracting mmCIF data as a crystal structure determination proceeds. This program extracts information about data collection, phasing, density modification, and the final structure refinement from the output files produced by many structure determination applications. The collected information is organized into an mmCIF file that is ready for deposition. Since PDB_EXTRACT fills in many data fields in this mmCIF file, fewer data items have to be manually entered which saves time and minimizes errors.
BLAST: www.ncbi.nih.gov/BLAST
4. USE LIGAND DEPOT
Ligand Depot is a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules. Ligand depot can be used to find codes for existing ligands, to link to other entries with a particular ligand, and to search for substructures. If a ligand related to a deposition is not in Ligand Depot, the chemical diagram, name, and formula can be emailed to deposit@rcsb.rutgers.edu
WEB: ligand-depot.rutgers.edu
PDB_EXTRACT is also part of the CCP4i interface. DESKTOP: deposit.pdb.org/software/PDB_EXTRACT WEB: pdb-extract.rutgers.edu
5. DEPOSIT YOUR STRUCTURE USING ADIT
ADIT checks, validates, and edits PDB structure data entries. ADIT contains separate views for X-ray, NMR, or cryo-EM structures. Information missing from uploaded files can be input using the ADIT tool editor. An mmCIF file can be written from desktop ADIT, and then uploaded into the Web version of ADIT or sent to the PDB for deposition.
2. CHECK YOUR STRUCTURE WITH THE PDB VALIDATION SUITE
The Validation Suite and Server is a set of tools used by the PDB for checking and processing structure data. Format consistency of coordinates can be checked and the structure can be validated before deposition. The validation report contains geometrical and experimental checks from the programs NUCheck1, PROCHECK2, and SFCHECK3. Sequence/coordinate alignment, missing and extra atoms or residues, and data inconsistencies are also reported here.
DESKTOP: deposit.pdb.org/software/ADIT WEB: deposit.pdb.org/adit (Rutgers-US) pdbdep.protein.osaka-u.ac.jp/adit (Osaka University, Japan)
DESKTOP: deposit.pdb.org/software/VAL WEB: deposit.pdb.org/validate
PDB ID. 1psi. Elliott, P. R., Lomas, D. A., Carrell, R. W., Abrahams, J. P.: Inhibitory conformation of the reactive loop of alpha 1-antitrypsin. Nat Struct Biol 3 pp. 676 (1996)