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2Q4J

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase

2Q4J の概要
エントリーDOI10.2210/pdb2q4j/pdb
関連するPDBエントリー2ICX 2ICY
分子名称Probable UTP-glucose-1-phosphate uridylyltransferase 2 (2 entities in total)
機能のキーワードensemble refinement, refinement methodology development, at3g03250, putative udp-glucose pyrophosphorylase, structural genomics, protein structure initiative, psi, center for eukaryotic structural genomics, cesg, transferase
由来する生物種Arabidopsis thaliana (thale cress)
細胞内の位置Cytoplasm (By similarity): Q9M9P3
タンパク質・核酸の鎖数2
化学式量合計103596.41
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: 2023-08-30)
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
Cited by
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
主引用文献が同じPDBエントリー
実験手法
X-RAY DIFFRACTION (1.863 Å)
構造検証レポート
Validation report summary of 2q4j
検証レポート(詳細版)ダウンロードをダウンロード

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件を2024-11-20に公開中

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