- PDB-3pzl: The crystal structure of agmatine ureohydrolase of Thermoplasma v... -
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基本情報
登録情報
データベース: PDB / ID: 3pzl
タイトル
The crystal structure of agmatine ureohydrolase of Thermoplasma volcanium
要素
Agmatine ureohydrolase
キーワード
HYDROLASE (加水分解酵素) / Structural Genomics (構造ゲノミクス) / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
機能・相同性
機能・相同性情報
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding 類似検索 - 分子機能
Agmatinase-related / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
解像度: 2.7→2.85 Å / 冗長度: 21.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4199 / % possible all: 100
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解析
ソフトウェア
名称
バージョン
分類
CBASS
データ収集
SOLVE
位相決定
REFMAC
5.5.0072
精密化
MOSFLM
データ削減
SCALA
データスケーリング
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.7→82.39 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.898 / SU B: 31.544 / SU ML: 0.303 / 交差検証法: THROUGHOUT / ESU R Free: 0.391 / 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
0.27105
1398
5.1 %
RANDOM
Rwork
0.21954
-
-
-
obs
0.22208
26146
93.94 %
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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
原子変位パラメータ
Biso mean: 59.624 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.48 Å2
1.24 Å2
0 Å2
2-
-
2.48 Å2
0 Å2
3-
-
-
-3.72 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.7→82.39 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
6840
0
6
50
6896
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
6967
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.373
1.972
9409
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.444
5
870
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
28.183
23.436
326
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.728
15
1200
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.9
15
57
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
1035
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
5305
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.972
1.5
4329
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.522
2
6977
X-RAY DIFFRACTION
r_scbond_it
2.538
3
2638
X-RAY DIFFRACTION
r_scangle_it
3.869
4.5
2432
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS精密化 シェル
解像度: 2.7→2.77 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.339
106
-
Rwork
0.239
2015
-
obs
-
4199
100 %
精密化 TLS
手法: refined / Origin x: -14.0693 Å / Origin y: -56.1216 Å / Origin z: -7.9033 Å