News
New Method Produces Record-breaking 860 PDB Structures
04/24
Scientists from SGC and UCB recently utilized Diamond Light Source to develop a new method to extract previously hidden information from the X-ray diffraction data that are measured when resolving the three-dimensional (3D) atomic structures of proteins and other biological molecules.
The new Pan-Dataset Density Analysis (PanDDA) method extracts the picture of the bound compound in exceptionally clear and unambiguous detail. PanDDA first identifies the source of the noise, and then removes it from the data. It exploits Diamond’s ability to repeat dozens to hundreds of measurements quickly, which are then characterized for differences between them, indicating the presence of bound compound, after which a noise correction is applied in 3D.
The results are published today in Nature Communications with the corresponding data publicly available in the PDB.
The 860 structures represent four protein targets, with 785 ground state structures and 75 ligand-bound structures. Explore the structures by searching “PanDDA analysis group deposition” at the RCSB PDB website or by using the links below:
- 9 entries of different ligands-bound to BAZ2B, Bromodomain adjacent to zinc finger domain protein 2B
- 24 entries of different ligands-bound to JMJD2D, Lysine-specific demethylase 4D
- 40 entries of different ligands-bound to BRD1, Bromodomain-containing protein 1
- 2 entries of different ligands-bound to SP100, Nuclear autoantigen Sp-100
- Full set of 860 entries
This set of structures is the largest submission to the PDB associated with a single publication. Working closely with the authors, the 860 structures were deposited in only 8 sessions using a new tool being developed by RCSB PDB.
The RCSB PDB Group Deposition system (GroupDep) supports automated depositions of large numbers of X-ray structures in parallel. It allows PDB depositors to take advantage of local templates and the PDB_extract program for batch processing, data packaging, upload, review, validation, and one-click submission of many closely related structures at once. Structures submitted via GroupDep can be received, biocurated, validated, and publicly released in a relatively short period of time.
GroupDep is being developed in part to support data coming from the NIH-NIGMS funded Drug Design Data Resource (D3R), which aims to advance the technology of computer-aided drug discovery through the interchange of high quality protein-ligand datasets and workflows, and by holding community-wide, blinded docking/scoring prediction challenges.
Depositors interested in testing the GroupDep system with a large dataset should contact [email protected].
For more information on this milestone, please see Game-changing PanDDA method unveils previously hidden 3D structure data at Diamond and Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density Nat. Commun. 8, 15123 doi: 10.1038/ncomms15123 (2017).
