2Q48

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g48480

2Q48 の概要

• エントリーDOI: 10.2210/pdb2q48/pdb
• 分子名称: Protein At5g48480 (2 entities in total)
• 機能のキーワード: ensemble refinement, refinement methodology development, at5g48480, reductively methylated protein, cath 3.10.180 fold, unknown function, dimer, structural genomics, protein structure initiative, psi, center for eukaryotic structural genomics, cesg
• 由来する生物種: Arabidopsis thaliana (thale cress)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 35337.21

構造登録者

Levin, E.J.,Kondrashov, D.A.,Wesenberg, G.E.,Phillips Jr., G.N.,Center for Eukaryotic Structural Genomics (CESG) (登録日: 2007-05-31, 公開日: 2007-06-19, 最終更新日: 2023-11-15)

主引用文献

Levin, E.J.,Kondrashov, D.A.,Wesenberg, G.E.,Phillips, G.N.
Ensemble refinement of protein crystal structures: validation and application.
Structure, 15:1040-1052, 2007

PubMed Abstract: X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

PubMed: 17850744
DOI: 10.1016/j.str.2007.06.019

実験手法

X-RAY DIFFRACTION (1.8 Å)