دورية أكاديمية
أعرض في EDS

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.

التفاصيل البيبلوغرافية
العنوان: Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.
المؤلفون: Zheng H; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA., Langner KM; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA., Shields GP; Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England., Hou J; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA., Kowiel M; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA., Allen FH; Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England., Murshudov G; MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England., Minor W; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA.
المصدر: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2017 Apr 01; Vol. 73 (Pt 4), pp. 316-325. Date of Electronic Publication: 2017 Mar 31.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: John Wiley & Sons Country of Publication: United States NLM ID: 101676043 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2059-7983 (Electronic) Linking ISSN: 20597983 NLM ISO Abbreviation: Acta Crystallogr D Struct Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: <2018-> : Medford, MA : John Wiley & Sons
Original Publication: [Malden, MA] : John Wiley & Sons, [2016]-
مواضيع طبية MeSH: Ferric Compounds/*chemistry , Ferrous Compounds/*chemistry , Heme/*chemistry , Hemoglobins/*chemistry, Crystallography, X-Ray ; Data Mining ; Humans ; Models, Molecular ; Oxidation-Reduction
مستخلص: The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valence R 0 parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal-organic bond-valence parameters. R 0 bond-valence parameters for iron(II), iron(III) and other metals have been optimized based on an automated processing of all CSD crystal structures. Almost all R 0 bond-valence parameters were reproduced, except for iron-nitrogen bonds, for which distinct R 0 parameters were defined for two observed subpopulations, corresponding to low-spin and high-spin states, of iron in both oxidation states. The significance of this data-driven method for parameter discovery, and how the spin state affects the interpretation of heme-containing proteins and iron-binding sites in macromolecular structures, are discussed.
References: Biochemistry. 2005 Jan 18;44(2):635-42. (PMID: 15641789)
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. (PMID: 21460454)
Chem Rev. 2009 Dec;109(12):6858-919. (PMID: 19728716)
Biochemistry. 1998 Nov 24;37(47):16459-64. (PMID: 9843411)
Acta Crystallogr B Struct Sci Cryst Eng Mater. 2016 Apr;72(Pt 2):171-9. (PMID: 27048719)
Acta Crystallogr B. 2000 Aug;56(Pt 4):565-9. (PMID: 10944245)
J Chem Theory Comput. 2008 Dec 9;4(12):2057-66. (PMID: 26620478)
Inorg Chem. 2011 May 16;50(10):4586-97. (PMID: 21506557)
Structure. 2000 Jul 15;8(7):775-88. (PMID: 10903944)
FEBS Lett. 1982 Oct 4;147(1):106-10. (PMID: 7140986)
Biochem Biophys Res Commun. 1985 Aug 30;131(1):98-102. (PMID: 4038310)
Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):32-7. (PMID: 12499536)
Nat Protoc. 2014 Jan;9(1):156-70. (PMID: 24356774)
Acta Crystallogr B. 2006 Oct;62(Pt 5):745-53. (PMID: 16983155)
Acta Crystallogr B. 2000 Jun;56 (Pt 3):455-65. (PMID: 10877354)
Acta Crystallogr B. 2002 Jun;58(Pt 3 Pt 1):380-8. (PMID: 12037359)
Acta Crystallogr B. 2004 Apr;60(Pt 2):174-8. (PMID: 15017089)
Phys Chem Chem Phys. 2009 Nov 21;11(43):10219-26. (PMID: 19865780)
J Inorg Biochem. 2008 Sep;102(9):1765-76. (PMID: 18614239)
J Mol Biol. 1984 May 15;175(2):159-74. (PMID: 6726807)
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. (PMID: 22505256)
Acta Crystallogr B. 2002 Jun;58(Pt 3 Pt 1):389-97. (PMID: 12037360)
Acta Crystallogr B. 2011 Aug;67(Pt 4):333-49. (PMID: 21775812)
معلومات مُعتمدة: MC_UP_A025_1012 United Kingdom MRC_ Medical Research Council; R01 GM117080 United States GM NIGMS NIH HHS; R01 GM117325 United States GM NIGMS NIH HHS; HHSN272201200026C United States AI NIAID NIH HHS; GM117325 United States GM NIGMS NIH HHS; GM117080 United States GM NIGMS NIH HHS
فهرسة مساهمة: Keywords: Cambridge Structural Database; bond-valence model; metal–organics; nonlinear conjugate gradients; oxidation state
المشرفين على المادة: 0 (Ferric Compounds)
0 (Ferrous Compounds)
0 (Hemoglobins)
42VZT0U6YR (Heme)
تواريخ الأحداث: Date Created: 20170405 Date Completed: 20171106 Latest Revision: 20231112
رمز التحديث: 20231112
مُعرف محوري في PubMed: PMC5503122
DOI: 10.1107/S2059798317000584
PMID: 28375143
قاعدة البيانات: MEDLINE
الوصف
تدمد:2059-7983
DOI:10.1107/S2059798317000584