Refined crystal structure of ferrocytochrome c2 from Rhodopseudomonas viridis at 1.6 A resolution.

The three-dimensional structure of ferrocytochrome c2 from the purple photosynthetic bacterium Rhodopseudomonas viridis has been refined to a final R-factor of 18.2% for 15,014 unique reflections collected by synchrotron radiation between 6.0 and 1.6 A resolution. The refined model includes 107 amino acid residues, one heme prosthetic group and 125 water molecules. The root-mean-square deviations from the ideal bond lengths and angles were 0.014 A and 3.0 degrees, respectively. The atomic coordinate error was estimated to be less than 0.3 A. A structure comparison of this cytochrome c2 with those of the other c-type cytochromes demonstrated that these cytochromes exhibit a high degree of structural similarity with the exception of the surface loop and the terminal region of the polypeptide chain. The deletion of an intrahelical amino residue distorted the conformation of the alpha-helix and it divided into two pieces. The C-terminal extension of the polypeptide chain caused significant conformational changes of the contact residues compared with the other c-type cytochromes. Of the water molecules conserved in various c-type cytochromes, two are located internally in the vicinity of the heme group. One of these water molecules found in this cytochrome c2 is evolutionarily conserved among eukaryotic cytochromes c. This water molecule is located in the heme proximate environment in a position similar to that of eukaryotic cytochromes c. The position of this water molecule is associated with the oxidation state of the heme iron in electron transfer.