8RXN
REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS
Summary for 8RXN
| Entry DOI | 10.2210/pdb8rxn/pdb |
| Descriptor | RUBREDOXIN, FE (III) ION, SULFATE ION, ... (4 entities in total) |
| Functional Keywords | electron transport(iron) |
| Biological source | Desulfovibrio vulgaris |
| Cellular location | Cytoplasm: P00269 |
| Total number of polymer chains | 1 |
| Total formula weight | 5730.08 |
| Authors | Dauter, Z.,Sieker, L.,Wilson, K. (deposition date: 1991-08-26, release date: 1993-10-31, Last modification date: 2024-02-14) |
| Primary citation | Dauter, Z.,Sieker, L.C.,Wilson, K.S. Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints. Acta Crystallogr.,Sect.B, 48:42-59, 1992 Cited by PubMed Abstract: X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha source. In both cases an imaging-plate scanner was used as detector. The space group of the crystals is P2(1) with cell dimensions a = 19.97, b = 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in the refinement. There were 18,532 independent X-ray observations for a total of 1916 atomic parameters. A round of unrestrained refinement gave an R factor of 16.0%, acceptable geometry for more than 90% of the protein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model. PubMed: 1616692DOI: 10.1107/S0108768191010613 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1 Å) |
Structure validation
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