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Title: Automated identification of elemental ions in macromolecular crystal structures

Journal Article · · Acta Crystallographica. Section D: Biological Crystallography (Online)
 [1];  [1];  [1];  [2];  [3];  [2];  [4];  [5];  [6]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
  2. Univ. of Cambridge (United Kingdom). Dept. of Haematology. Cambridge Inst. for Medical Research. Wellcome Trust
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL); Joint Center for Structural Genomics (United States). http://www.jcsg.org
  4. Duke Univ., Durham, NC (United States). Medical Center. Dept. of Biochemistry
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  6. Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
+ Show Author Affiliations

Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625714
Journal Information:
Acta Crystallographica. Section D: Biological Crystallography (Online), Vol. 70, Issue 4; ISSN 1399-0047
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 34 works
Citation information provided by
Web of Science

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Cited By (10)

Finding high-quality metal ion-centric regions across the worldwide Protein Data Bank posted_content January 2019
Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders—a critical PDB survey journal November 2018
Structural Basis for the Allosteric Regulation of the SbtA Bicarbonate Transporter by the P II -like Protein, SbtB, from Cyanobium sp. PCC7001 journal November 2019
Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank journal September 2019
Structural basis for the allosteric regulation of the SbtA bicarbonate transporter by the P II -like protein, SbtB, from Cyanobium sp. PCC7001 posted_content July 2019
Sample manipulation and data assembly for robust microcrystal synchrotron crystallography journal July 2018
High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage journal March 2019
Crystal structures of sialyltransferase from Photobacterium damselae journal November 2014
New Biological Insights from Better Structure Models journal March 2016
Mg 2+ ions: do they bind to nucleobase nitrogens? journal December 2016

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Biophysics
Crystallography