Conformation change of cytochrome c: I. Ferrocytochrome c structure refined at 1·5 Å resolution

Abstract

Tuna ferrocytochrome c has been crystallographically refined at a resolution of 1.5 Å using the Diamond real-space method followed by Jack-Levitt restrained energy and reciprocal space refinement, monitoring progress continuously with superimposed Fourier and difference Fourier maps: The final R factor for cytochrome plus 53 solvent molecules, using 13,840 reflections with intensities greater than 2 σ, is 17·3%. The overall structure remains as described earlier (Takano et al., 1977), but structural details have been clarified to the point where meaningful comparison can be made with the oxidized molecule (following paper). Main and side-chain flexibility as judged by isotropic temperature parameters correlate with position in the molecule, with greatest flexibility at external chain loops. The haem group is held tightly in place by its attachments and neighbours, and is deformed slightly into a saddle shape. The iron does not deviate significantly from the best mean plane of the haem, and bond lengths to ligands are as expected from model compounds. A water molecule buried in the haem crevice is bonded to Asn52, Tyr67 and Thr78, the latter two being bonded also to Met80 and the outer haem propionate. It is proposed that this buried water molecule is involved in the reduction of ferricytochrome c by chromous ion, and the reactions of Tyr67 with KI 3 and tetranitromethane. Two other buried water molecules occur beneath the 20's loop at the right, and within the 40's loop at the bottom. Reasonable if tentative functional assignments can be made for all 24 of the evolutionarily invariant residues in the cytochrome molecule.