- PDB-3dcz: CRYSTAL STRUCTURE OF A PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPOR... -
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データベース: PDB / ID: 3dcz
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPORT COMPLEX (TM0246) FROM THERMOTOGA MARITIMA AT 1.65 A RESOLUTION
要素
putative RnfG subunit of electron transport complex
キーワード
OXIDOREDUCTASE / PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPORT COMPLEX / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
機能・相同性
機能・相同性情報
トランスロカーゼ / FMN binding / membrane => GO:0016020 / electron transfer activity / plasma membrane 類似検索 - 分子機能
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 30-224 OF THE FULL LENGTH PROTEIN.
モノクロメーター: Single crystal Si(111) bent monochromator (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
0.91162
1
2
0.97932
1
3
0.97891
1
反射
解像度: 1.65→29.148 Å / Num. obs: 25591 / % possible obs: 100 % / 冗長度: 3.7 % / Biso Wilson estimate: 18.735 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.5
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
1.65-1.69
3.7
0.497
1.5
6885
1876
0.497
100
1.69-1.74
3.7
0.404
1.9
6662
1808
0.404
100
1.74-1.79
3.7
0.319
2.4
6524
1772
0.319
100
1.79-1.84
3.7
0.266
2.9
6336
1717
0.266
100
1.84-1.91
3.7
0.217
3.5
6206
1680
0.217
100
1.91-1.97
3.7
0.163
4.4
5907
1612
0.163
100
1.97-2.05
3.7
0.133
5.6
5804
1558
0.133
100
2.05-2.13
3.7
0.11
6.7
5499
1491
0.11
100
2.13-2.22
3.7
0.093
7.6
5399
1464
0.093
100
2.22-2.33
3.7
0.093
7.5
5146
1390
0.093
100
2.33-2.46
3.7
0.092
6.9
4829
1319
0.092
100
2.46-2.61
3.6
0.086
7.5
4520
1240
0.086
100
2.61-2.79
3.6
0.076
8.8
4306
1184
0.076
100
2.79-3.01
3.7
0.062
10.2
4054
1108
0.062
100
3.01-3.3
3.7
0.051
11.6
3760
1027
0.051
100
3.3-3.69
3.6
0.043
14.2
3338
922
0.043
100
3.69-4.26
3.6
0.041
14.5
2989
828
0.041
100
4.26-5.22
3.6
0.037
16
2520
705
0.037
100
5.22-7.38
3.5
0.041
15.2
1994
569
0.041
100
7.38-29.15
3.3
0.041
14.5
1045
321
0.041
97.5
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位相決定
位相決定
手法: 多波長異常分散
-
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
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: 1.65→29.148 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.023 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.086 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. 4. SO4,ACT,EDO MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.205
1304
5.1 %
RANDOM
Rwork
0.176
-
-
-
obs
0.177
25581
99.94 %
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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: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータ
Biso mean: 16.063 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.07 Å2
0 Å2
0 Å2
2-
-
-0.35 Å2
0 Å2
3-
-
-
0.28 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.65→29.148 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1294
0
18
145
1457
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
1404
X-RAY DIFFRACTION
r_bond_other_d
0.005
0.02
959
X-RAY DIFFRACTION
r_angle_refined_deg
1.481
2.01
1915
X-RAY DIFFRACTION
r_angle_other_deg
0.898
3
2364
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.308
5
190
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.765
24.107
56
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.606
15
247
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.145
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
224
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1552
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
273
X-RAY DIFFRACTION
r_nbd_refined
0.216
0.2
268
X-RAY DIFFRACTION
r_nbd_other
0.199
0.2
969
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
673
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
744
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.156
0.2
128
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.261
0.2
21
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.314
0.2
25
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.163
0.2
18
X-RAY DIFFRACTION
r_mcbond_it
2.053
3
906
X-RAY DIFFRACTION
r_mcbond_other
0.489
3
356
X-RAY DIFFRACTION
r_mcangle_it
2.989
5
1433
X-RAY DIFFRACTION
r_scbond_it
4.256
8
553
X-RAY DIFFRACTION
r_scangle_it
6.114
11
470
LS精密化 シェル
解像度: 1.65→1.693 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.263
105
-
Rwork
0.223
1771
-
all
-
1876
-
obs
-
-
100 %
精密化 TLS
手法: refined / Origin x: 31.2107 Å / Origin y: 35.4521 Å / Origin z: 18.5391 Å