Fowler, N.J. orcid.org/0000-0002-6005-935X, Sljoka, A. and Williamson, M.P. orcid.org/0000-0001-5572-1903 (2021) The accuracy of NMR protein structures in the Protein Data Bank. Structure, 29 (12). 1430-1439.e2. ISSN 0969-2126
Abstract
The program ANSURR measures the accuracy of NMR structures by comparing rigidity obtained from experimental backbone chemical shifts and from structures. We report on ANSURR analysis of 7,000 PDB NMR ensembles within the Protein Data Bank, which can be found at ansurr.com. The accuracy of NMR structures progressively improved up until 2005, but since then, it has plateaued. Most structures have accurate secondary structure, but are generally too floppy, particularly in loops. Thus, there is a need for more experimental restraints in loops. Currently, the best predictors of accuracy are Ramachandran distribution and the number of NOE restraints per residue. The precision of structures within the ensemble correlates well with accuracy, as does the number of hydrogen bond restraints per residue. Structure accuracy is improved when other components (such as additional polypeptide chains or ligands) are included.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2021 Elsevier Ltd. This is an author produced version of a paper subsequently published in Structure. Uploaded in accordance with the publisher's self-archiving policy. Article available under the terms of the CC-BY-NC-ND licence (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
Keywords: | NMR; protein structure; rigidity; experimental restraints; validation; chemical shift; PDB |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Molecular Biology and Biotechnology (Sheffield) |
Funding Information: | Funder Grant number BIOTECHNOLOGY AND BIOLOGICAL SCIENCES RESEARCH COUNCIL BB/P020038/1 |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 28 Jan 2022 11:19 |
Last Modified: | 30 Jul 2022 00:13 |
Status: | Published |
Publisher: | Elsevier BV |
Refereed: | Yes |
Identification Number: | 10.1016/j.str.2021.07.001 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:183017 |