2DVH

THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES

2DVH の概要

• エントリーDOI: 10.2210/pdb2dvh/pdb
• NMR情報: BMRB: 4208
• 分子名称: CYTOCHROME C-553, HEME C (2 entities in total)
• 機能のキーワード: electron transport, cytochrome c, heme
• 由来する生物種: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough
• 細胞内の位置: Periplasm: P04032
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 8843.94

構造登録者

Sebban-Kreuzer, C.,Blackledge, M.J.,Dolla, A.,Marion, D.,Guerlesquin, F. (登録日: 1998-03-25, 公開日: 1998-06-17, 最終更新日: 2024-10-23)

主引用文献

Blackledge, M.J.,Medvedeva, S.,Poncin, M.,Guerlesquin, F.,Bruschi, M.,Marion, D.
Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics.
J.Mol.Biol., 245:661-681, 1995

PubMed Abstract: The solution structure of Desulfovibrio vulgaris Hildenborough (DvH) ferrocytochrome c553 has been determined by nuclear magnetic resonance spectroscopy and combined simulated annealing/high temperature restrained molecular dynamics calculations. This three-stage protocol consists of an initial determination of overall fold from randomised co-ordinates, followed by a 20 picosecond exploratory stage, during which the non-bonded terms are simplified to facilitate as broad a sampling of conformational space as possible, and a 26 picosecond refinement stage, using the full AMBER force field. This latter stage systematically improved the energetic and convergence characteristics of the ensemble, while still satisfying the experimental restraints. Forty structures have been obtained from a total of 875 distance constraints for this protein of 79 amino acid residues. The root-mean-square deviation over all residues with respect to the mean is 0.70(+/- 0.12)A for the backbone (N, C alpha and C') atoms. Two conformations of the turn motif at the solvent/heme cleft interface have been identified, both fulfilling the experimental data and having equally viable energetic characteristics. The stability of the ensemble and the dynamic characteristics have been further investigated by subjecting ten of the structures to constraint-free molecular dynamics calculations (130 picoseconds) in vacuo. The structures were found to be stable to within 1.5 A of the initial backbone conformation. Comparison with the dynamic behaviour of the restrained molecular dynamics calculations has been used to identify regions of inherent flexibility in the molecule.

PubMed: 7844834
DOI: 10.1006/jmbi.1994.0054

実験手法

SOLUTION NMR