3F6S

Desulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin alternate conformers

3F6S の概要

• エントリーDOI: 10.2210/pdb3f6s/pdb
• 関連するPDBエントリー: 3F6R
• 分子名称: Flavodoxin, FLAVIN MONONUCLEOTIDE (3 entities in total)
• 機能のキーワード: flavodoxin-like fold, fmn binding, oxidized, electron transport, flavoprotein, fmn, transport
• 由来する生物種: Desulfovibrio desulfuricans
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 129301.85

構造登録者

Guelker, M.,Shamoo, Y. (登録日: 2008-11-06, 公開日: 2009-06-09, 最終更新日: 2024-04-03)

主引用文献

Guelker, M.,Stagg, L.,Wittung-Stafshede, P.,Shamoo, Y.
Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin.
Acta Crystallogr.,Sect.D, 65:523-534, 2009

PubMed Abstract: The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3(1)21 and P4(3), at 2.5 and 2.0 A resolution, respectively. Structure determination in space group P3(1)21 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3(1)21 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P4(3), which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3(1)21 crystal form. During the early stages of refinement, application of the appropriate twin law, (-h, -k, l), was required to converge to reasonable R-factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition.

PubMed: 19465766
DOI: 10.1107/S0907444909010075

実験手法

X-RAY DIFFRACTION (2.502 Å)