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Title: 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.

Authors:
ORCiD logo; ORCiD logo
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. doi:https://doi.org/10.1107/S205979831801519X
Moriarty, Nigel W., and Adams, Paul D. Fri . "Iron–sulfur clusters have no right angles". United Kingdom. doi: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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: https://doi.org/10.1107/S205979831801519X

Citation Metrics:
Cited by: 2 works
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    Works referencing / citing this record:

    Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
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