1IR0

OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (FORM II)

1IR0 の概要

• エントリーDOI: 10.2210/pdb1ir0/pdb
• 関連するPDBエントリー: 1IQZ
• 分子名称: Ferredoxin, SULFATE ION, IRON/SULFUR CLUSTER, ... (4 entities in total)
• 機能のキーワード: ferredoxin, iron-sulfer protein, ultlahigh resolution analysis, geometry of [4fe-4s] cluster, electron transport
• 由来する生物種: Bacillus thermoproteolyticus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 9413.42

構造登録者

Fukuyama, K.,Okada, T.,Kakuta, Y.,Takahashi, Y. (登録日: 2001-08-30, 公開日: 2002-02-13, 最終更新日: 2023-10-25)

主引用文献

Fukuyama, K.,Okada, T.,Kakuta, Y.,Takahashi, Y.
Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein.
J.Mol.Biol., 315:1155-1166, 2002

PubMed Abstract: Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 A and 1.00 A resolutions, respectively, at 100 K using synchrotron radiation. Anisotropic temperature factors were introduced for all non-hydrogen atoms in the refinement with SHELX-97, in which stereochemical restraints were applied to the protein chain but not to the [4Fe-4S] cluster. The final crystallographic R-factors are 9.8 % for 7.0-0.92 A resolution data of the form I and 11.2 % for the 13.3-1.0 A resolution data of the form II. Many hydrogen atoms as well as multiple conformations for several side-chains have been identified. The present refinement has revised the conformations of several peptide bonds and side-chains assigned previously at 2.3 A resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C(alpha)-C bond of Lys2. Although the overall structures in the two crystal forms are very similar, conformational differences are observed in the two residues at the middle (Glu29 and Asp30) and the C-terminal residues, which have large temperature factors. The [4Fe-4S] cluster is a distorted cube with non-planar rhombic faces. Slight but significant compression of the four Fe-S bonds along one direction is observed in both crystal forms, and results in the D(2d) symmetry of the cluster. The compressed direction of the cluster relative to the protein is conserved in the two crystal forms and consistent with that in one of the clusters in Clostridium acidurici ferredoxin.

PubMed: 11827483
DOI: 10.1006/jmbi.2001.5292

実験手法

X-RAY DIFFRACTION (1 Å)