RCSB PDB Data Validation and Deposition Services


SF-Tool | pdb_extract | Validation Server | ADIT deposition tool | ADIT-NMR | NEW!Emdep/EM-ADIT | Try new ADITBeta! | NEW!Ligand Expo | NEW!Deposition Services FAQ

Welcome to the RCSB PDB Deposition Portal. For other deposition servers (PDBj, PDBe), please visit the wwPDB page.
Returning users can begin by using the quick links above.


The following data deposition tools and instructions can make your structure deposition easy, complete and accurate:

  1. Check the announcements to be familiar with the latest format and deposition policy changes.
  2. Gather information about the proteins/nucleic acids in your structure from sequence databases (e.g. using UniProtKB 1 or BLAST 2 ) or about your ligand (using Ligand Expo, formerly Ligand Depot 3 ). If you wish to deposit a new ligand, instructions will be provided during deposition.
  3. Convert and Check your crystallographic structure factors with our SF-Tool, including SFcheck and sf-convert among other tools, if appropriate. The deposited structure factor file should be the one that was used for the final refinement. This can either be in mmCIF, ASCII, or mtz formats and should at least include h, k, l, K, SigmaF (and/or I and SigmaI) and test flags. Definitions and format are available in DOC (48 KB) and PDF (24 KB) format.
  4. Prepare your structural data for deposition using pdb_extract 4 and/or the desktop version of ADIT.

    5. THEN

  5. Validate your structure using our Validation Server. Structures solved by NMR are currently limited to model coordinate validations.
  6. Deposit your structure using the structure deposition tool ADIT or ADIT-NMR.

    OR

  7. Validate and Deposit with one tool: ADITBeta!

The Validation Server can also be used to monitor improvements made to your structural model before you begin the deposition process.

Detailed step-by-step instructions for individual structural methods are available.

Tutorials for first-time and experienced depositors:
 
Policies and Procedures

Announcements

2/18/10 - Changes to the wwPDB Policy for Depositing Polypeptide Structures

The wwPDB now accepts polypeptide structure depositions of all gene products; all naturally-occuring, non-ribosomally synthesized peptides, such as antibiotics; and all peptidic repeat units of larger polymers, such as fibrous and amyloid polymers. In addition, non-naturally occurring synthetic peptides with at least 24 residues will be accepted for deposition.


Consistent with earlier policy, depositions of polynucleotide and polysaccharide structures of 4 or more residues are also accepted. For more information, see the wwPDB Policy Guide at http://www.wwpdb.org/policy.html


12/2/08 - A new standardized version of the PDB archive to be released

A new standardized version of the PDB archive will be available from ftp://ftp.wwpdb.org in early 2009. All entries released prior to December 2, 2008 will be re-released as PDB Format Version 3.15 files. This release will overwrite all existing files. A snapshot of the archive before this release will be available from ftp://snapshots.wwpdb.org/. For documentation, please see www.wwpdb.org/docs.html Questions may be sent to info@wwpdb.org.


11/25/08 - New releases to follow format guide version 3.20

Beginning December 2, 2008, all newly-released PDB entries will follow PDB File Format Contents Guide Version 3.20 (PDF | HTML). This format includes site and assembly annotation, and supports the nomenclature introduced in 2007 in the Chemical Component Dictionary. The Version 3.20 Changes Guide highlights the lists changes in format from 3.1. Please send any questions to info@wwpdb.org.


05/05/08 - We are happy to announce the release of the new RCSB PDB Deposition Portal!

Improvements to the layout and instructions make the deposition process easier to understand and complete, with deposition tool interfaces (pdb_extract, ADIT, etc.) also being updated shortly. We have also improved our Crystallographic Data Validation tool and turned it into SF-Tool, which offers online versions of sfcheck and our structure factor conversion tool, sf-convert, along with other useful tools specifically for X-ray structures.


05/05/08 - We are also happy to announce the next version of Ligand Depot, Ligand EXPO!

It is not only faster for you to find your ligand of interest, but you can easily search for related chemical components and interactively view the ligand within their PDB entries (click here for an example of caffeine (CFF); you must have Java enabled). A sketching tool is provided where you can upload a variety of 2D structure files (including REFMAC monomer sketcher library files) for conversion to mmCIF (or other) formats, and a new Browse feature that lets you search for and interactively view today's most important molecules.


During the annotation of structures the numbering and chain IDs of chemical groups and waters may be changed in accordance with the wwPDB chain ID rules. Thus deposition and processing of structures prior to preparation of the manuscript will ensure consistent usage of chain IDs and residue numbers in the manuscript and the PDB file.


Effective February 1, 2008, structure factor amplitudes/intensities (for crystal structures) and restraints (for NMR structures) are a mandatory requirement for PDB deposition. This policy is published at http://www.wwpdb.org/news.html.


The status of all entries is updated every Tuesday at 12 noon EST. All new entries deposited during the previous week (before Friday 8am EST) will be searchable following the update. The searchable status information includes title, author names and deposition date. The current status of experimental data, coordinates, and sequence is also available.


If modifications (REVDATs) need to be made to entries released as part of the Remediation Project after August 1, 2007, the re-released files will follow Contents Guide Version 3.1.


Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.



1 The UniProt Consortium. (2008) "The Universal Protein Resource (UniProt)." Nucleic Acids Res. 36:D190-D195.
2 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.
3 Feng, Z., Chen, L., Maddula, H., Akcan, O., Oughtred, R., Berman, H.M., & Westbrook, J. (2004) " Ligand Depot: a data warehouse for ligands bound to macromolecules " Bioinformatics 20:2153-2155.
4 Yang, H., Guranovic, V., Dutta, S., Feng, Z., Berman, H.M., & Westbrook, J.D. (2004) " Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. " Acta Cryst. D60, 1833-1839.