Iron–sulfur clusters have no right angles
Abstract
Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the Fe4S4cubane-type cluster was created using the Cambridge Structural Database (CSD) and high-resolution structures from the Protein Data Bank. Geometries from each source were compared and pairs of refinements were performed to validate these new restraints. In addition to the restraints internal to the cluster, the CSD was mined to generate bond and angle restraints to be applied to the most common linking motif for Fe4S4: coordination of the four Fe atoms to the side-chain sulfurs of four cysteine residues. Furthermore, computational tools were developed to assist researchers when refining Fe4S4-containing proteins.
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Institutes of Health (NIH)
- OSTI Identifier:
- 1489724
- Alternate Identifier(s):
- OSTI ID: 1580354
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Acta Crystallographica. Section D. Structural Biology
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Volume: 75 Journal Issue: 1; Journal ID: ISSN 2059-7983
- Publisher:
- IUCr
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; macromolecular refinement; iron–sulfur clusters; restraints
Citation Formats
Moriarty, Nigel W., and Adams, Paul D. Iron–sulfur clusters have no right angles. United Kingdom: N. p., 2019.
Web. doi:10.1107/S205979831801519X.
Moriarty, Nigel W., & Adams, Paul D. Iron–sulfur clusters have no right angles. United Kingdom. https://doi.org/10.1107/S205979831801519X
Moriarty, Nigel W., and Adams, Paul D. Fri .
"Iron–sulfur clusters have no right angles". United Kingdom. https://doi.org/10.1107/S205979831801519X.
@article{osti_1489724,
title = {Iron–sulfur clusters have no right angles},
author = {Moriarty, Nigel W. and Adams, Paul D.},
abstractNote = {Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the Fe4S4cubane-type cluster was created using the Cambridge Structural Database (CSD) and high-resolution structures from the Protein Data Bank. Geometries from each source were compared and pairs of refinements were performed to validate these new restraints. In addition to the restraints internal to the cluster, the CSD was mined to generate bond and angle restraints to be applied to the most common linking motif for Fe4S4: coordination of the four Fe atoms to the side-chain sulfurs of four cysteine residues. Furthermore, computational tools were developed to assist researchers when refining Fe4S4-containing proteins.},
doi = {10.1107/S205979831801519X},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 1,
volume = 75,
place = {United Kingdom},
year = {2019},
month = {1}
}
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https://doi.org/10.1107/S205979831801519X
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Works referenced in this record:
Validation and extraction of molecular-geometry information from small-molecule databases
journal, February 2017
- Long, Fei; Nicholls, Robert A.; Emsley, Paul
- Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2
Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures
journal, March 2008
- Macrae, Clare F.; Bruno, Ian J.; Chisholm, James A.
- Journal of Applied Crystallography, Vol. 41, Issue 2
Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: Thermostability and electron transfer
journal, November 2000
- Nogi, T.; Fathir, I.; Kobayashi, M.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 25
Crystallography Open Database – an open-access collection of crystal structures
journal, May 2009
- Gražulis, Saulius; Chateigner, Daniel; Downs, Robert T.
- Journal of Applied Crystallography, Vol. 42, Issue 4
The Crystal Structure of Fe 4 S 4 Quinolinate Synthase Unravels an Enzymatic Dehydration Mechanism That Uses Tyrosine and a Hydrolase-Type Triad
journal, February 2014
- Cherrier, Mickaël V.; Chan, Alice; Darnault, Claudine
- Journal of the American Chemical Society, Vol. 136, Issue 14
AceDRG : a stereochemical description generator for ligands
journal, February 2017
- Long, Fei; Nicholls, Robert A.; Emsley, Paul
- Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2
Structure, function and evolution of bacterial ferredoxins
journal, April 1988
- Bruschi, Mireille; Guerlesquin, Françoise
- FEMS Microbiology Letters, Vol. 54, Issue 2
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
journal, December 2014
- Westbrook, John D.; Shao, Chenghua; Feng, Zukang
- Bioinformatics, Vol. 31, Issue 8
electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation
journal, September 2009
- Moriarty, Nigel W.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 10
New software for searching the Cambridge Structural Database and visualizing crystal structures
journal, May 2002
- Bruno, Ian J.; Cole, Jason C.; Edgington, Paul R.
- Acta Crystallographica Section B Structural Science, Vol. 58, Issue 3
Ultrahigh-resolution structure of high-potential iron–sulfur protein from Thermochromatium tepidum
journal, June 2002
- Liu, Lijun; Nogi, Terukazu; Kobayashi, Masayuki
- Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 7
The Cambridge Structural Database
journal, April 2016
- Groom, Colin R.; Bruno, Ian J.; Lightfoot, Matthew P.
- Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials, Vol. 72, Issue 2, p. 171-179
Mercury : visualization and analysis of crystal structures
journal, May 2006
- Macrae, Clare F.; Edgington, Paul R.; McCabe, Patrick
- Journal of Applied Crystallography, Vol. 39, Issue 3
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
An editor for the generation and customization of geometry restraints
journal, February 2017
- Moriarty, Nigel W.; Draizen, Eli J.; Adams, Paul D.
- Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2
REFMAC 5 dictionary: organization of prior chemical knowledge and guidelines for its use
journal, November 2004
- Vagin, Alexei A.; Steiner, Roberto A.; Lebedev, Andrey A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12
Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012
- Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Structural analysis of cubane-type iron clusters
journal, July 2013
- Tan, Lay Ling; Holm, R. H.; Lee, Sonny C.
- Polyhedron, Vol. 58