2OED

GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings

2OED の概要

• エントリーDOI: 10.2210/pdb2oed/pdb
• 関連するPDBエントリー: 1IGD 1P7E 1P7F
• 分子名称: Immunoglobulin G-binding protein G (1 entity in total)
• 機能のキーワード: immune system, residual dipolar couplings
• 由来する生物種: Streptococcus sp. 'group G'
• 細胞内の位置: Secreted, cell wall; Peptidoglycan-anchor (Potential): P19909
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 6214.85

構造登録者

Ulmer, T.S.,Ramirez, B.E.,Delaglio, F.,Bax, A.,Grishaev, A. (登録日: 2006-12-29, 公開日: 2007-01-30, 最終更新日: 2023-12-27)

主引用文献

Ulmer, T.S.,Ramirez, B.E.,Delaglio, F.,Bax, A.
Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy
J.Am.Chem.Soc., 125:9179-9191, 2003

PubMed Abstract: NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the (13)C(alpha)-(13)C' and (13)C'-(15)N dipolar couplings improves the agreement between experimental and predicted (15)N-(1)H(N) as well as (13)C(alpha)-(1)H(alpha) dipolar couplings. Evaluation of the peptide bond N-H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle omega from 180 degrees and the angle between the N-H vector and the C'-N-C(alpha) plane. The slope of this correlation is -1, indicating that, on average, pyramidalization of the peptide N contributes to small deviations from peptide bond planarity ( = 179.3 +/- 3.1 degrees ) to the same degree as true twisting around the C'-N bond. Although hydrogens are commonly built onto crystal structures assuming the N-H vector orientation falls on the line bisecting the C'-N-C(alpha) angle, a better approximation adjusts the C(alpha)-C'-N-H torsion angle to -2 degrees. The (15)N-(1)H(N) dipolar data do not contradict the commonly accepted motional model where angular fluctuations of the N-H bond orthogonal to the peptide plane are larger than in-plane motions, but the amplitude of angular fluctuations orthogonal the C(alpha)(i-1)-N(i)-C(alpha)(i) plane exceeds that of in-plane motions by at most 10-15 degrees. Dipolar coupling analysis indicates that for most of the GB3 backbone, the amide order parameters, S, are highly homogeneous and vary by less than +/-7%. Evaluation of the H(alpha) proton positions indicates that the average C(alpha)-H(alpha) vector orientation deviates by less than 1 degrees from the direction that makes ideal tetrahedral angles with the C(alpha)-C(beta) and C(alpha)-N vectors.

PubMed: 15369375
DOI: 10.1021/ja0350684

実験手法

SOLUTION NMR