Deposition/Biocuration and Archiving Services

In the first quarter of 2018, 2971 experimentally-determined structures were deposited to the PDB archive. Data are processed by wwPDB partners RCSB PDB, PDBe, and PDBj.

Of the structures deposited in 2018 so far, 88.2% were deposited with a release status of hold until publication; 7.6% were released as soon as annotation of the entry was complete; and 4.2% were held until a particular date. 87.3% of these entries were determined by X-ray crystallographic methods; 4.3% were determined by NMR methods.

During the same quarter, 2582 structures and 438 EMDB maps were released in the PDB.

Database has published an article describing Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

All data deposited to the PDB undergo critical review by wwPDB biocurators. Structural data submitted are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources, and validated for scientific/technical accuracy.

Biocuration is integral to PDB data archiving, as it facilitates accurate, consistent, and comprehensive representation of biomolecular structure data, which in turn allows efficient and effective usage by research scientists, educators, students, and the curious public worldwide.

This paper describes the importance of biocuration for structural biology data deposited to the PDB, wwPDB biocuration processes, and the role of expert biocurators in sustaining a high-quality archive.

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y. Young, John D. Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M. Berrisford, G. Jawahar Swaminathan, Thomas J. Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R. Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R. Clark, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand Gore, Vladimir Guranovic, Pieter M. S. Hendrickx, Brian P. Hudson, Yasuyo Ikegawa, Yumiko Kengaku, Catherine L. Lawson, Yuhe Liang, Lora Mak, Abhik Mukhopadhyay, Buvaneswari Narayanan, Kayoko Nishiyama, Ardan Patwardhan, Gaurav Sahni, Eduardo Sanz-García, Junko Sato, Monica R. Sekharan, Chenghua Shao, Oliver S. Smart, Lihua Tan, Glen van Ginkel, Huanwang Yang, Marina A. Zhuravleva, John L. Markley, Haruki Nakamura, Genji Kurisu, Gerard J. Kleywegt, Sameer Velankar, Helen M. Berman, Stephen K. Burley

(2018) Database 2018: bay002 doi: 10.1093/database/bay002

Validation reports for all PDB structures have been updated to include new percentile statistics reflecting the state of the archive on December 31st 2017 and updated versions of third-party software: CCP4/Refmac (7.0 v44), Phenix (1.13) and Mogul (2018) and CSD archive (as539be). The LLDF statistic previously used to identify ligands that do not fit electron density well has been replaced by a combination of Real-space R-factor (RSR>0.4) and Real-space correlation coefficient (RSCC<0.8). The identification of standard amino acid or nucleotide residues that do not fit the electron density well has been corrected to take into account how reliably Refmac software reproduces the R-factors reported by authors. Documentation at wwpdb.org/validation has been updated to reflect these changes.

Updated reports are accessible from:

• ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)
• ftp://ftp.rcsb.org/pub/pdb/validation_reports/ (RCSB PDB)
• ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)
• ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj)

A copy of the previous version is archived at RCSB PDB and PDBj.

wwPDB validation reports provide an assessment of structure quality using widely accepted standards and criteria, recommended by community experts serving in Validation Task Forces. The wwPDB partners strongly encourage journal editors and referees to request them from authors as part of the manuscript submission and review process. The reports are date-stamped and display the wwPDB logo, and contain the same information, regardless of which wwPDB site processed the entry. Provision of wwPDB validation reports is already required by Nature, eLife, The Journal of Biological Chemistry, the International Union of Crystallography (IUCr) journals, FEBS journals, Journal of Immunology and Angew Chem Int Ed Engl as part of their manuscript-submission process.

Validation reports are also provided to depositors through OneDep validation, deposition and biocuration of structure data. The wwPDB partners encourage the use of the stand-alone validation server and the web service API at any time prior to data deposition. Depositors are required to review and accept the reports as part of the data submission process. Validation reports will continue to be developed and improved as we receive recommendations from the expert Validation Task Forces for X-ray, NMR, EM, experts on ligand validation, and as we collect feedback from depositors and users.

An article focused on the structure validation reports produced by wwPDB is available:

Validation of Structures in the Protein Data Bank (2017) Structure 25: 1317-1318 doi: 10.1016/j.str.2017.10.009.