2006 Deposition Statistics

In the first quarter of 2006, 1775 structures were deposited to the PDB archive.

The entries were processed by the wwPDB teams at RCSB-Rutgers, MSD-EBI, and PDBj. Of the structures deposited, 71% were deposited with a release status of "hold until publication"; 17% were released as soon as annotation of the entry was complete; and 10% were held until a particular date.

82% of these entries were determined by X-ray crystallographic methods; 11% were determined by NMR methods; and 82 % of these depositions were deposited with experimental data.

Validating structures saves deposition time

To lower the number of revisions and problems found during the annotation process, depositors should validate their structure, provide the correct and complete sequence, and run BLAST[1].

The Validation Server allows the user to check the format of coordinate and structure factor files, and to create a variety of validation reports about a structure. When the validation process is complete, users are presented with a validation report which includes an Atlas entry, a summary report, and a collection of structural diagnostics including bond distance and angle comparisons, torsion angle comparisons, base morphology comparisons (for nucleic acids), and an image of the molecule. Reports from MolProbity[2], PROCHECK[3], NUCheck, and SFCheck[4] are made available. Validating a structure using this tool helps authors spot possible errors in the structure prior to starting a deposition session.

Structures can also be validated using ADIT by selecting the 'validate' option before proceeding to 'deposit' option.

It is also important to provide the complete and correct sequence for polymers. The deposited sequence should include all residues in the crystal or NMR tube used for the experiment, including uncleaved His tags and cloning artifacts and any residues missing from the coordinates due to lack of electron density or disorder. The one letter code sequence should not conflict with the sequence from the coordinates.

Annotators perform a BLAST to find a match for the deposited sequence with a sequence database reference. Based on these search results, sequence database records are generated in the PDB entry. If the deposited sequence is in conflict with the known database sequence, records are created in the entry with the proper explanation of the conflict. Running BLAST on the sequence prior to deposition can help authors find possible mismatches. If the polymer has engineered mutations they should be mentioned in the "Molecule Details, Specific mutation" section of ADIT for proper annotation.

Providing the correct and complete sequence, running a BLAST search and validating the structure help make the annotation process fast and easy as well as each PDB entry complete and accurate.

  1. Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., Helmberg, W., Kenton, D.L., Khovayko, O., Lipman, D.J., Madden, T.L., Maglott, D.R., Ostell, J., Pontius, J.U., Pruitt, K.D., Schuler, G.D., Schriml, L.M., Sequeira, E., Sherry, S.T., Sirotkin, K., Starchenko, G., Suzek, T.O., Tatusov, R., Tatusova, T.A., Wagner, L., and Yaschenko, E. (2005). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 33, D39-45.
  2. Davis, I.W., Murray, L.W., Richardson, J.S., and Richardson, D.C. (2004). MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32, W615-619.
  3. Laskowski, R.A., Rullmann, J.A., MacArthur, M.W., Kaptein, R., and Thornton, J.M. (1996). AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486.
  4. Vaguine, A.A., Richelle, J., and Wodak, S.J. (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 D Biol Crystallogr 55, 191-205.