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Modeling the structure of pyrococcus furiosus rubredoxin by homology to other X‐ray structures
Author(s) -
Wampler John E.,
Bradley Elizabeth A.,
Adams MICHAEL W.W.,
Stewart David E.
Publication year - 1993
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560020414
Subject(s) - pyrococcus furiosus , desulfovibrio vulgaris , rubredoxin , crystallography , homology (biology) , homology modeling , crystal structure , chemistry , protein structure , biology , amino acid , biochemistry , bacteria , archaea , enzyme , genetics , gene
The three‐dimensional structure of rubredoxin from the hyperthermophilic archaebacterium, Pyrococcus furiosus , has been modeled from the X‐ray crystal structures of three homologous proteins from Clostridium pasteurianum, Desulfovibrio gigas , and Desulfovibrio vulgaris. All three homology models are similar. When comparing the positions of all heavy atoms and essential hydrogen atoms to the recently solved crystal structure (Day, M.W., et al., 1992, Protein Sci. 1 , 1494–1507) of the same protein, the homology models differ from the X‐ray structure by 2.09 Å root mean square (RMS). The X‐ray and the zinc‐substituted NMR structures (Blake, P.R., et al., 1992b, Protein Sci. 1 , 1508–1521) show a similar level of difference (2.05 Å RMS). On average, the homology models are closer to the X‐ray structure than to the NMR structures (2.09 vs. 2.42 Å RMS).