- PDB-3m4a: Crystal structure of a bacterial topoisomerase IB in complex with... -
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基本情報
登録情報
データベース: PDB / ID: 3m4a
タイトル
Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site
要素
DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3')
DNA (5'-D(*GP*CP*GP*CP*CP*CP*TP*TP*AP*TP*TP*C)-3')
Putative Type I topoisomerase
キーワード
Isomerase/DNA / type IB / topIB / protein-DNA complex / Isomerase-DNA complex
機能・相同性
機能・相同性情報
DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA binding 類似検索 - 分子機能
Topoisomerase I; Chain A, domain 4 - #120 / : / Bacterial DNA topoisomerase IB, N-terminal domain / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type ...Topoisomerase I; Chain A, domain 4 - #120 / : / Bacterial DNA topoisomerase IB, N-terminal domain / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type / Eukaryotic DNA topoisomerase I, catalytic core / DNA breaking-rejoining enzyme, catalytic core / Topoisomerase I; Chain A, domain 4 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
ACETIC ACID / DNA / DNA (> 10) / DNA topoisomerase 類似検索 - 構成要素
温度: 283 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5 詳細: 30% PEG 400 (w/v), 0.1 M sodium acetate (pH 4.5), 0.2 M calcium chloride. 1:1 molar ratio of protein and DNA, VAPOR DIFFUSION, HANGING DROP, temperature 283K
解像度: 1.65→19.824 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.617 / SU ML: 0.057 / 交差検証法: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.22169
2820
5 %
RANDOM
Rwork
0.19344
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all
0.19487
58613
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obs
0.19487
53565
96.16 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK