- PDB-2ou6: Crystal structure of a putative metalloenzyme of the duf664 famil... -
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基本情報
登録情報
データベース: PDB / ID: 2ou6
タイトル
Crystal structure of a putative metalloenzyme of the duf664 family (dr_1065) from deinococcus radiodurans at 1.80 A resolution
要素
Hypothetical protein
キーワード
METAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
Protein of unknown function DUF664 / Protein of unknown function (DUF664) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / NICKEL (II) ION / Uncharacterized protein
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE.
モノクロメーター: Single crystal Si(111) bent (horizontal focusing) プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID
波長 (Å)
相対比
1
0.97905
1
2
0.97932
1
3
0.91837
1
反射
解像度: 1.8→125 Å / Num. obs: 22207 / % possible obs: 91.1 % / 冗長度: 6.9 % / Biso Wilson estimate: 21.72 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 7.1
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
1.8-1.85
2.6
0.268
2.5
2678
1047
0.268
61.4
1.85-1.9
3
0.237
2.7
3766
1244
0.237
74.1
1.9-1.95
3.8
0.219
2.8
5100
1340
0.219
82
1.95-2.01
5.2
0.203
3.1
7047
1364
0.203
83.7
2.01-2.08
5.1
0.16
3.9
7020
1372
0.16
87.5
2.08-2.15
5
0.133
4.5
6977
1383
0.133
92
2.15-2.23
5.2
0.119
5.1
7278
1404
0.119
94.9
2.23-2.32
5.3
0.108
5.4
7344
1383
0.108
98.4
2.32-2.43
5.6
0.096
6.2
7663
1362
0.096
99.6
2.43-2.55
6
0.095
6.3
7769
1293
0.095
99.9
2.55-2.68
6.6
0.093
6.4
8380
1262
0.093
100
2.68-2.85
7.3
0.086
7
8669
1192
0.086
100
2.85-3.04
7.9
0.077
7.8
9090
1145
0.077
100
3.04-3.29
8.8
0.066
8.9
9158
1043
0.066
100
3.29-3.6
10.2
0.062
9.6
10158
999
0.062
100
3.6-4.02
12.6
0.062
9.3
11380
901
0.062
100
4.02-4.65
14.4
0.061
10.2
11680
809
0.061
100
4.65-5.69
14
0.061
9.7
9936
711
0.061
100
5.69-8.05
13.3
0.066
8.6
7754
581
0.066
100
8.05-125.43
10.3
0.058
10.2
3843
372
0.058
98.3
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位相決定
位相決定
手法: 多波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
MolProbity
3beta29
モデル構築
SHELX
位相決定
REFMAC
5.2.0005
精密化
SCALA
データスケーリング
PDB_EXTRACT
2
データ抽出
MAR345
CCD
データ収集
MOSFLM
データ削減
CCP4
(SCALA)
データスケーリング
SHELXD
位相決定
autoSHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.8→125 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.232 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. NI MODELED BASED ON GEOMETRY AND HOMOLOGS. 5. SO4 AND GOL MODELED BASED ON CRYSTALLIZATION CONDITIONS. 6. THERE IS UNMODELED DENSITY NEAR PHE 120 AND TRP 160.
Rfactor
反射数
%反射
Selection details
Rfree
0.188
1137
5.1 %
RANDOM
Rwork
0.155
-
-
-
all
0.157
-
-
-
obs
0.157
22101
91.06 %
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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: 19.024 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.32 Å2
-0.66 Å2
0 Å2
2-
-
-1.32 Å2
0 Å2
3-
-
-
1.98 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.8→125 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1428
0
23
266
1717
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
1517
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1354
X-RAY DIFFRACTION
r_angle_refined_deg
1.548
1.947
2083
X-RAY DIFFRACTION
r_angle_other_deg
0.912
3
3130
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.626
5
192
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.358
23.867
75
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.829
15
217
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.484
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.102
0.2
227
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
1718
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
315
X-RAY DIFFRACTION
r_nbd_refined
0.217
0.2
322
X-RAY DIFFRACTION
r_nbd_other
0.185
0.2
1293
X-RAY DIFFRACTION
r_nbtor_refined
0.181
0.2
754
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
805
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.161
0.2
201
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.136
0.2
12
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.303
0.2
49
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.089
0.2
11
X-RAY DIFFRACTION
r_mcbond_it
2.02
3
998
X-RAY DIFFRACTION
r_mcbond_other
0.505
3
373
X-RAY DIFFRACTION
r_mcangle_it
2.609
5
1489
X-RAY DIFFRACTION
r_scbond_it
4.621
8
653
X-RAY DIFFRACTION
r_scangle_it
6.492
11
589
LS精密化 シェル
解像度: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.251
73
-
Rwork
0.175
973
-
obs
-
1046
60.71 %
精密化 TLS
手法: refined / Origin x: 13.647 Å / Origin y: 39.193 Å / Origin z: 2.493 Å