Worldwide Protein Data Bank validation information: usage and trends.

Oliver S Smart,Swanand Gore,Radka Svobodová Vařeková,Veronika Bendová,Sameer Velankar,Vladimír Horský,Gerard J Kleywegt

doi:10.1107/s2059798318003303

Abstract

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrendsDB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

Highlights

The Protein Data Bank is the single global archive of experimentally determined three-dimensional structures of biological macromolecules
An additional red bar shows the percentage of residues with RSRZ outliers, i.e. residues that show a poorer than expected fit to the electron density. This is followed by a table highlighting outliers for small-molecule ligands, which contains information about any issues with chirality when compared with the standard Worldwide Protein Data Bank (wwPDB) Chemical Component Dictionary (CCD; Westbrook et al, 2015), outliers in geometry as highlighted using Mogul analysis, close contacts and issues with experimental evidence: electron density in the case of X-ray crystallographic structures, as assessed by local ligand density fit (LLDF) analysis
The archive is managed by the wwPDB, an international collaboration of four partner sites: RCSB Protein Data Bank (PDB) and Biological Magnetic Resonance Data Bank (BMRB) in the USA, Protein Data Bank Japan (PDBj) in Japan and Protein Data Bank in Europe (PDBe) in Europe

Summary

Introduction

The Protein Data Bank is the single global archive of experimentally determined three-dimensional structures of biological macromolecules. An additional red bar shows the percentage of residues with RSRZ outliers, i.e. residues that show a poorer than expected fit to the electron density This is followed by a table highlighting outliers for small-molecule ligands, which contains information about any issues with chirality when compared with the standard wwPDB Chemical Component Dictionary (CCD; Westbrook et al, 2015), outliers in geometry as highlighted using Mogul analysis, close contacts and issues with experimental evidence: electron density in the case of X-ray crystallographic structures, as assessed by local ligand density fit (LLDF) analysis (for a detailed examination of ligand validation, see Smart et al, 2018). The introduction of VRs for X-ray, NMR and 3DEM structures has fulfilled the goals of wider acceptance of the recommended validation metrics, improved data quality at the time of deposition and helped reviewers, readers and structure users to assess the quality of coordinate models and experimental data

Using validation information

ValTrendsDB

Discussion and conclusions

Findings

Funding information