- PDB-3dl1: Crystal structure of a Putative Metal-dependent Hydrolase (YP_001... -
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基本情報
登録情報
データベース: PDB / ID: 3dl1
タイトル
Crystal structure of a Putative Metal-dependent Hydrolase (YP_001336084.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.20 A resolution
要素
Putative Metal-dependent Hydrolase
キーワード
HYDROLASE / YP_001336084.1 / A Putative Metal-dependent Hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Protein of unknown function (DUF980) / unknown function
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE TARGET PROTEIN SEQUENCE MATCHES TO GENBANK ENTRY YP_001336084.1.YP_001336084.1, COMPARED TO UNP MATCH A6TB83, HAS AN EXTRA RESIDEU MET AT THE BEGINNING OF THE SEQUENCE.
モノクロメーター: Single crystal Si(111) bent monochromator (horizontal focusing) プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
相対比: 1
反射
解像度: 2.2→29.311 Å / Num. obs: 17061 / % possible obs: 99.9 % / 冗長度: 7.1 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 5.9
反射 シェル
Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.2-2.26
7.3
0.678
1.1
8841
1212
0.678
100
2.26-2.32
7.3
0.458
1.6
8965
1230
0.458
100
2.32-2.39
7.2
0.413
1.8
8345
1152
0.413
100
2.39-2.46
7.4
0.322
2.3
8366
1133
0.322
100
2.46-2.54
7.2
0.29
2.6
7954
1104
0.29
100
2.54-2.63
7.3
0.221
3.4
7921
1079
0.221
100
2.63-2.73
7.2
0.186
3.9
7439
1035
0.186
100
2.73-2.84
7.3
0.141
5.2
7428
1014
0.141
100
2.84-2.97
7.2
0.118
6.1
6802
948
0.118
100
2.97-3.11
7.3
0.097
7.2
6768
931
0.097
100
3.11-3.28
7.2
0.089
7.5
6192
865
0.089
100
3.28-3.48
7.2
0.078
8.3
5956
833
0.078
100
3.48-3.72
7.1
0.073
8.5
5699
802
0.073
100
3.72-4.02
7
0.071
8.5
5179
740
0.071
100
4.02-4.4
7
0.058
10
4783
687
0.058
100
4.4-4.92
6.9
0.053
11.3
4319
622
0.053
100
4.92-5.68
6.8
0.057
9.9
3855
568
0.057
100
5.68-6.96
6.5
0.064
9.5
3147
482
0.064
100
6.96-9.84
6.3
0.052
11
2503
395
0.052
100
9.84-29.31
5.3
0.047
13.3
1220
229
0.047
95.2
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位相決定
位相決定
手法: 単波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
SCALA
データスケーリング
PDB_EXTRACT
3.004
データ抽出
MOSFLM
データ削減
SHARP
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.2→29.311 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 8.619 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.15 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
Rfactor
反射数
%反射
Selection details
Rfree
0.202
861
5.1 %
RANDOM
Rwork
0.171
-
-
-
obs
0.172
16997
99.74 %
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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: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータ
Biso mean: 37.533 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.14 Å2
0 Å2
0 Å2
2-
-
1.14 Å2
0 Å2
3-
-
-
-2.29 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.2→29.311 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1664
0
1
97
1762
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1731
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1147
X-RAY DIFFRACTION
r_angle_refined_deg
1.375
1.946
2366
X-RAY DIFFRACTION
r_angle_other_deg
0.928
3
2787
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.983
5
213
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.303
23.571
84
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.22
15
263
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.88
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
262
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1936
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
366
X-RAY DIFFRACTION
r_nbd_refined
0.209
0.2
337
X-RAY DIFFRACTION
r_nbd_other
0.183
0.2
1146
X-RAY DIFFRACTION
r_nbtor_refined
0.178
0.2
825
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
852
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.159
0.2
67
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.185
0.2
6
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.335
0.2
15
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.079
0.2
5
X-RAY DIFFRACTION
r_mcbond_it
2.144
3
1154
X-RAY DIFFRACTION
r_mcbond_other
0.464
3
416
X-RAY DIFFRACTION
r_mcangle_it
3.215
5
1704
X-RAY DIFFRACTION
r_scbond_it
5.566
8
737
X-RAY DIFFRACTION
r_scangle_it
7.315
11
659
LS精密化 シェル
解像度: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.31
61
-
Rwork
0.241
1144
-
all
-
1205
-
obs
-
-
99.34 %
精密化 TLS
手法: refined / Origin x: 50.6167 Å / Origin y: 23.6789 Å / Origin z: 8.5781 Å