In 2014, PDBx/mmCIF became the PDB’s archive format and the the legacy PDB file format was frozen. In addition to PDBx/mmCIF files for all entries, wwPDB produces PDB format-formatted files for entries that can be represented in this legacy file format (e.g., entries with over 99,999 atoms or with multi-character chain IDs are only available in PDBx/mmCIF)
As the size and complexity of PDB structures increases, additional limitations of the legacy PDB format are becoming apparent and need to be addressed.
Restrictions in the SHEET record fields in legacy the PDB file format do not allow for the generation of complex beta sheet topology. Complex beta sheet topologies include instances where beta strands are part of multiple beta sheets and other cases where the definition of the strands within a beta sheet cannot be presented in a linear description. For example, in PDB entry 5wln a large beta barrel structure is created from multiple copies of a single protein; within the beta sheet forming the barrel are instances of a single beta strand making contacts on one side with multiple other strands, even from different chains.
This limitation, however, is not an issue in the PDBx/mmCIF formatted file, where these complex beta sheet topology can be captured in _struct_sheet, _struct_sheet_order, _struct_sheet_range, and _struct_sheet_hbond.
Starting June 8th 2021, legacy PDB format files will no longer be generated for PDB entries where the SHEET topology cannot be generated. For these structures, wwPDB will continue to provide secondary structure information with helix and sheet information in the PDBx/mmCIF formatted file.
wwPDB regularly reviews the software used during OneDep biocuration. The _struct_site and _struct_site_gen categories in PDBx/mmCIF (SITE records in the legacy PDB file format) are generated by in-house software and based purely upon distance calculations, and therefore may not reflect biological functional sites.
Starting in June 2021, the in-house legacy software which produces _struct_site and _struct_site_gen records will be retired and wwPDB will no longer generate these categories for newly-deposited PDB entries. Existing entries will be unaffected.
wwPDB validation reports provided in OneDep now include restraints validation for NMR entries to help users identify potential discrepancies in their data. Recommendations from the wwPDB NMR Validation Task Force (VTF) on how restraints data should be validated have been published (10.1016/j.str.2013.07.021). Since then, wwPDB has been working with the NMR community to develop the NMR Exchange Format (NEF) dictionary (10.1038/nsmb.3041) to enable validation of restraints data. In March 2020, OneDep was configured to accept NMR experimental data (chemical shifts and restraints) as a single file, either in NMR-STAR or NEF format. Now, NMR restraints data validation has been incorporated into the wwPDB validation package. Validation Reports generated in OneDep have been extended to include NMR restraints analysis in when restraints are deposited in either NEF or NMR-STAR format. The contents of restraints analysis in the wwPDB validation reports include conformationally restricting restraints, residual restraint violations, average number of distance and dihedral angle restraint violations per model, and distance and dihedral angle violation analysis for each model and ensemble with graphical and tabular statistics. These features should help both depositors and users to identify potential errors in NMR data. For more details, including example validation reports, please see the news item at the wwPDB site here.
The new entries are available the metabolomics section of our web page. You can view the available fragments by following this link. These data from the DSI-poised screening fragment library have been provided by the COVID19-NMR project.
The 2020 Nobel Prize in chemistry was awarded to Emmanuelle Charpentier (Max Planck Unit for the Science of Pathogens, Berlin, Germany) and Jennifer A. Doudna (University of California, Berkeley, USA) "for the development of a method for genome editing" for their work on CRISPR/Cas9. BMRB would like to congratulate them on their incredible work.
BMRB has several entries with NMR data for Cas9, which can be seen here.
BMRB announces that the NMR-STAR v2.1 format will no longer be supported by BMRB after September 1, 2020. This will mean that all data from BMRB will be available in NMR-STAR versions 3.1 or higher. BMRB has been providing data in NMR-STAR v3.1 format for over ten years, and if you are not sure which version you are using, it is likely that you are already using v3.1 and that this change will not affect you. Users that need to convert older files to the new format, as well as developers whose software reads and/or writes NMR-STAR v2.1 files are invited to contact our help desk at firstname.lastname@example.org for help and orientation on updating files and/or support for the new format. The NMR-STAR format has evolved over the years, with the current format having improved data organization, enhanced metadata support, expanded data content, and enriched inter-operation with closely related data resources like the wwPDB, of which BMRB is a Core Archive for NMR experimental data.
BMRB announces the planned discontinuation of the ADIT-NMR deposition system. Depositors with open depositions started on ADIT-NMR should finish them by September 1, 2020. ADIT-NMR will no longer allow new depositions to be started beginning June 1, 2020. Depositors are encouraged to start new depositions using BMRBdep.
BMRBdep provides a streamlined, more responsive deposition experience, as well as better support for depositors, with a familiar but cleaner interface. Please contact BMRB’s help desk at email@example.com if you envision any problems with an open deposition due to this timeline.