- PDB-4qgl: Acireductone dioxygenase from Bacillus anthracis with three cadmi... -
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基本情報
登録情報
データベース: PDB / ID: 4qgl
タイトル
Acireductone dioxygenase from Bacillus anthracis with three cadmium ions
要素
Acireductone dioxygenase
キーワード
OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / RmlC-like cupin / Iron Binding / 1 / 2-dihydroxy-5-(methylthio)pent-1-en-3-one dioxygenase
機能・相同性
機能・相同性情報
acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / nickel cation binding / iron ion binding 類似検索 - 分子機能
Acireductone dioxygenase ARD, bacteria / Acireductone dioxygenase ARD family / ARD/ARD' family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta 類似検索 - ドメイン・相同性
解像度: 2.61→19.85 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.321 / SU ML: 0.2 / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.071 / 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
0.2257
251
4.7 %
RANDOM
Rwork
0.17605
-
-
-
obs
0.17848
5103
84.74 %
-
all
-
5103
-
-
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: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータ
Biso mean: 30.418 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.14 Å2
0 Å2
7.51 Å2
2-
-
-26.62 Å2
-0 Å2
3-
-
-
25.48 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.61→19.85 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1399
0
3
32
1434
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.019
1430
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1346
X-RAY DIFFRACTION
r_angle_refined_deg
1.539
1.936
1941
X-RAY DIFFRACTION
r_angle_other_deg
0.845
3
3092
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.15
5
173
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.598
24.667
75
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.967
15
241
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.497
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.087
0.2
216
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1634
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
338
LS精密化 シェル
解像度: 2.605→2.672 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.328
17
-
Rwork
0.267
325
-
obs
-
325
76.68 %
精密化 TLS
手法: refined / Origin x: 34.887 Å / Origin y: 30.494 Å / Origin z: 19.618 Å