Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms

The structures of two crystal forms (form I, P3₂21, a = b = 43.7, c = 50.7 Å; form II, P2₁, a = 27.3, b = 44.9, c = 51.2 Å and β = 90.6°) of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved by the molecular-replacement method. Form I has been refined at a resolution of 2.0 Å to an R value of 20.8% and includes 32 water molecules. Form II includes 86 water molecules and has been refined at 1.9 Å resolution to an R value of 17.5%. In form II, there are three molecules in the asymmetric unit with the molecules related by a non-crystallographic 3₂ symmetry axis. In both crystal forms, it was found that only a few residues effectively participate in the formation of intermolecular contacts along both the crystallographic (form I) and the non-crystallographic (form II) 3₂ axes. The crystal structure of the form II crystal is compared with those of other rubredoxin molecules from anaerobic bacteria. From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has been revealed.