Newsletter | Winter 2017 ⋅ Number 72

Data Deposition and Annotation

In the fourth quarter of 2016, 2754 experimentally-determined structures were deposited to the PDB archive for a total of 11,614 entries deposited in the year. In 2015, 10,958 entries were deposited.

Of all structures deposited this year, 91.3% were determined by X-ray crystallographic methods; 4.1% were determined by NMR methods. 85.7% were deposited with a release status of hold until publication; 8.9% were released as soon as annotation of the entry was complete; and 5.4% were held until a particular date.

10,899 new PDB structures were released in 2016. They account for 8.7% of the yearend total holdings of 125,463.

The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project have collaborated to update the experimental methods descriptions of all electron microscopy and electron crystallography-derived structures in the PDB archive. With this work now completed, all 3DEM-derived entries have better-organized content and conform to the revised data model developed by the EMDataBank team for use within the wwPDB OneDep System. The OneDep System has supported deposition, annotation, and validation of 3DEM structures and fully integrates deposition of 3DEM maps and model coordinates since January 2016.

Examples of 3DEM model files (both remediated and from the OneDep system) are provided in a new wwPDB ftp directory ( A data-item level description of the changes made during remediation is provided (XLS). 3DEM terms in the updated PDBx/mmCIF dictionary are available for review.

Files in the current PDB ftp archive will be replaced with new files corresponding to the updated PDBx/mmCIF dictionary in 2017. Users are encouraged to review and test the example data files.

In January 2014, the wwPDB launched a unified deposition, annotation, and validation system (now called OneDep) for structures determined using X-ray crystallography that has used to submit and biocurate tens of thousands of PDB structures. OneDep uses the PDBx/mmCIF data format, which produces more uniform data, supports replacement of data files pre- and post-deposition, enhances communication with depositors, enables improved annotation, and provides validation reports based on recommendations from wwPDB expert task forces.
A version of OneDep that supporting structures determined by X-ray crystallography, NMR, and 3DEM was launched January 8 2016. The extended system is integrated with the repositories for NMR and 3DEM experimental data and can assign both BMRB and EMDB accession codes.

In the Fall, the legacy deposition systems, AutoDep, ADIT-NMR and EMDep were closed to new PDB and EMDB submissions.  An updated ADIT-NMR system (available from BMRB and PDBj-BMRB) will continue to accept NMR data associated with a structure currently not accepted by the unified wwPDB deposition system (for example, relaxation data, and primary time-domain spectra) as well as experimental NMR data not associated with the deposition of 3D coordinates.

Data deposition, validation, and annotation highlights included:

  • The new OneDep system received 10,955 entries (10113 X-ray, 355 NMR, 458 3DEM, 1 NMR-EM hybrid) and released 9412 PDB entries into the PDB archive.
  • Ligand Validation Workshop White Paper Published:  The inaugural ligand validation meeting brought co-crystal structure determination experts from academe and industry together with X-ray Crystallography and Computational Chemistry software developers to discuss and develop best practices for validation of co-crystal structures; editorial/refereeing standards for publishing co-crystal structures; and recommendations for ligand representation across the archive. These recommendations have been published: Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop (2016) Structure 24: 502508 doi: 10.1016/j.str.2016.02.017.
  • Following the successful implementation usage of Validation Reports for X-ray crystallographic entries in the PDB, Validation Reports for NMR and 3DEM structures were made available.
  • To enable better annotation and tracking, OneDep began to accept ORCID identifiers and information on relevant grant funding during data submission.