2RDV

RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM

Summary for 2RDV

• Entry DOI: 10.2210/pdb2rdv/pdb
• Descriptor: RUBREDOXIN, FE (III) ION (3 entities in total)
• Functional Keywords: rubredoxin, compnd, electron transfer protein, metalloprotein, sulfate-reducing bacterium, electron transfer
• Biological source: Desulfovibrio vulgaris str. 'Miyazaki F'
• Cellular location: Cytoplasm: P15412
• Total number of polymer chains: 3
• Total formula weight: 16974.25

Authors

Higuchi, Y.,Yasuoka, N. (deposition date: 1998-10-07, release date: 1999-05-18, Last modification date: 2024-05-22)

Primary citation

Misaki, S.,Morimoto, Y.,Ogata, M.,Yagi, T.,Higuchi, Y.,Yasuoka, N.
Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.
Acta Crystallogr.,Sect.D, 55:408-413, 1999

PubMed Abstract: The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7 A; form II, P21, a = 27.3, b = 44.9, c = 51.2 A and beta = 90. 6 degrees ) 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 A 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 A 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.

PubMed: 10089348
DOI: 10.1107/S0907444998011810

Experimental method

X-RAY DIFFRACTION (1.9 Å)