Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome c3, from Desulfovibrio vulgaris Hildenborough at 2 Å Resolution1

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 Å 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=43.17Å, b = 62.91 Å, c=41.17Å, orthorhombic, P2₁2₁2₁ 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 Å. 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.