Data Deposition/Biocuration Services and Archive Management

In the fourth quarter of 2018, 3,034 experimentally-determined structures were deposited to the PDB archive for a total of 12,179 entries deposited in the year.

Of all structures deposited this year, 87.6% were deposited with a release status of hold until publication; 7.6% were released as soon as annotation of the entry was complete; and 4.8% were held until a particular date. 87.1% of these entries were determined by X-ray crystallographic methods; 3.4% were determined by NMR methods; and 9.1% by 3DEM.

11,247 new PDB structures were released in 2018. They account for 7.6% of the year-end total holdings of 147,610 available entries.

The OneDep system for deposition, validation, and biocuration recently extended the range of metadata collected for structures solved by X-ray Free-Electron Laser (XFEL) and Serial Femtosecond Crystallography (SFX). Depositors can now provide details of the sample delivery, data measurement details such as focusing optics, pulse energy, frequency, and number of crystals used in new PDBx/mmCIF categories dedicated to XFEL and SFX experiments. Authors of existing XFEL entries in the PDB archive will be contacted to provide additional information for their entries.

Methods for Determining Atomic Structures: Structures of photoactive yellow protein were determined by serial femtosecond crystallography after illumination, capturing the isomerization of the chromophore after it absorbs light. Structures included in this movie include: 5hd3 (ground state), 5hdc (100-400 femtoseconds after illumination), 5hdd (800-1200 femtoseconds), 5hds (3 picoseconds), 4b9o (100 picoseconds), 5hd5 (200 nanoseconds) and 1ts0 (1 millisecond). For more, see the Molecule of the Month on Photoactive Yellow Protein.

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
(2018) Database 2018: bay002 doi: 10.1093/database/bay002