8RXN

REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS

8RXN の概要

• エントリーDOI: 10.2210/pdb8rxn/pdb
• 分子名称: RUBREDOXIN, FE (III) ION, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: electron transport(iron)
• 由来する生物種: Desulfovibrio vulgaris
• 細胞内の位置: Cytoplasm: P00269
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 5730.08

構造登録者

Dauter, Z.,Sieker, L.,Wilson, K. (登録日: 1991-08-26, 公開日: 1993-10-31, 最終更新日: 2024-02-14)

主引用文献

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

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: 1616692
DOI: 10.1107/S0108768191010613

実験手法

X-RAY DIFFRACTION (1 Å)