- PDB-1d6m: CRYSTAL STRUCTURE OF E. COLI DNA TOPOISOMERASE III -
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基本情報
登録情報
データベース: PDB / ID: 1d6m
タイトル
CRYSTAL STRUCTURE OF E. COLI DNA TOPOISOMERASE III
要素
DNA TOPOISOMERASE III
キーワード
ISOMERASE / DNA TOPOISOMERASE / DECATENATING ENZYME
機能・相同性
機能・相同性情報
cytoplasmic replication fork / sequence-specific single stranded DNA binding / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA-templated DNA replication / DNA recombination / DNA repair / magnesium ion binding 類似検索 - 分子機能
DNA topoisomerase III / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 ...DNA topoisomerase III / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / Topoisomerase I; domain 3 / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Distorted Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
解像度: 3→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 24861467.8 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber 詳細: Refinement done with REFMAC. The solvent correction was calculated with XPLOR and applied in REFMAC. Final parameters obtained with CNS 0.4
Rfactor
反射数
%反射
Selection details
Rfree
0.268
1643
5 %
RANDOM
Rwork
0.237
-
-
-
all
0.239
32569
-
-
obs
0.239
32569
93.6 %
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原子変位パラメータ
Biso mean: 51.9 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.92 Å2
8.16 Å2
0 Å2
2-
-
1.92 Å2
0 Å2
3-
-
-
-3.84 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.43 Å
0.37 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.61 Å
0.44 Å
精密化ステップ
サイクル: LAST / 解像度: 3→10 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
4798
0
0
0
4798
拘束条件
Refine-ID
タイプ
Dev ideal
X-RAY DIFFRACTION
p_angle_d
2.3
X-RAY DIFFRACTION
p_bond_d
0.007
LS精密化 シェル
解像度: 3→3.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6