2CYM

EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION

Summary for 2CYM

• Entry DOI: 10.2210/pdb2cym/pdb
• Descriptor: CYTOCHROME C3, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: electron transport
• Biological source: Desulfovibrio vulgaris
• Cellular location: Periplasm: P00131
• Total number of polymer chains: 1
• Total formula weight: 14153.41

Authors

Morimoto, Y.,Tani, T.,Okumura, H.,Higuchi, Y.,Yasuoka, N. (deposition date: 1993-09-29, release date: 1994-04-30, Last modification date: 2024-02-14)

Primary citation

Morimoto, Y.,Tani, T.,Okumura, H.,Higuchi, Y.,Yasuoka, N.
Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution.
J.Biochem.(Tokyo), 110:532-540, 1991

PubMed Abstract: The three-dimensional structure of cytochrome c3 from Desulfovibrio vulgaris Hildenborough has been determined by use of the molecular replacement method and refined at 2.0 A resolution. A suitable crystal of the cytochrome c3 was obtained from buffer solution (25 mM Tris-HCl, pH 7.4), with 75% ethanol as the precipitating reagent. Crystallographic data are as follows: a = 43.17 A, b = 62.91 A, c = 41.17 A, orthorhombic, P2(1)2(1)2(1) and Z = 4. Constrained least-squares refinement and a molecular dynamics procedure with a simulated structure annealing method yielded a crystallographic R-factor of 0.212. The similarity in the folding pattern of both cytochromes c3 is established, the mean deviation of the polypeptide backbone between the two structures being 0.367 A. Most of the amino acids substitutions from DvMF were located on the surface of the molecule, and in particular, S27 and V86 were placed near the propionic acid of the heme group so as to hang over the heme and the cleft of the molecule.

PubMed: 1663945

Experimental method

X-RAY DIFFRACTION (2 Å)