High resolution crystal structure of ferricytochrome c′ from Rhodobacter sphaeroides

Cytochrome c′ isolated from Rhodobacter sphaeroides strain R26 (RSCP) crystallizes as a dimer of two identical 14-kDa subunits, in trigonal space group P31, with cell parameters a, b = 48.10 Å, c = 115.80 Å. The crystal structure of RSCP has been solved by molecular replacement using cytochrome c′ from Rhodobacter capsulatus (PDB ID: 1CPQ) as a search model. To ensure effective phase bias removal, the RSCP model was iteratively built into maps generated by a modified wARP procedure, Shake&wARP. The 1.8 Å model (PDB ID: 1GQA) has been refined to an R = 0.204 and freeR = 0.254. Each subunit consists of four antiparallel α-helices, with the pentacoordinate heme covalently bound to a C–X–Y–C–H motif near the C-terminus. F14, located on helix A, blocks direct access to what would be the sixth “distal” ligand binding site of the heme. The dimer subunits form a flattened “X” shape, intermediate between the Type 1 and Type 2 cytochromes c′. The presence of the aromatic F14 and a deep channel between helices B and C places RSCP into Group 1 cytochromes c′. Clear electron density has revealed that the amino acid sequences for the cytochrome c′ from strains R26 and 2.4.1 are identical.