- PDB-5w74: Crystal Structure of the Group II Chaperonin from Methanococcus M... -
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基本情報
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データベース: PDB / ID: 5w74
タイトル
Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis D386ADeltaLid Mutant in the Open, ADP-Bound State
要素
Chaperonin
キーワード
CHAPERONE / chaperonin / complex / atpase
機能・相同性
機能・相同性情報
ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding 類似検索 - 分子機能
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
波長: 1 Å / 相対比: 1
反射
解像度: 3.65→49.589 Å / Num. obs: 96789 / % possible obs: 97.4 % / 冗長度: 15.5 % / CC1/2: 0.997 / Net I/σ(I): 11.3
反射 シェル
解像度: 3.65→3.71 Å / 冗長度: 11.5 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4255 / CC1/2: 0.329 / % possible all: 88.7
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解析
ソフトウェア
名称
バージョン
分類
iMOSFLM
dataprocessing
Aimless
データ削減
PHASER
位相決定
PHENIX
(1.11.1_2575: ???)
精密化
精密化
構造決定の手法: 分子置換 / 解像度: 3.65→49.589 Å / SU ML: 0.52 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 30.95
Rfactor
反射数
%反射
Rfree
0.2746
4823
4.99 %
Rwork
0.2648
-
-
obs
0.2653
96563
97.08 %
溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップ
サイクル: LAST / 解像度: 3.65→49.589 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
28408
0
224
0
28632
拘束条件
Refine-ID
タイプ
Dev ideal
数
X-RAY DIFFRACTION
f_bond_d
0.002
28784
X-RAY DIFFRACTION
f_angle_d
0.531
38784
X-RAY DIFFRACTION
f_dihedral_angle_d
10.562
10976
X-RAY DIFFRACTION
f_chiral_restr
0.04
4784
X-RAY DIFFRACTION
f_plane_restr
0.003
4960
LS精密化 シェル
解像度 (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.65-3.6915
0.4119
151
0.4131
2742
X-RAY DIFFRACTION
88
3.6915-3.7349
0.3846
142
0.386
2713
X-RAY DIFFRACTION
87
3.7349-3.7804
0.3573
135
0.3737
2701
X-RAY DIFFRACTION
88
3.7804-3.8283
0.3783
165
0.3657
2779
X-RAY DIFFRACTION
89
3.8283-3.8786
0.3643
144
0.3656
2845
X-RAY DIFFRACTION
92
3.8786-3.9317
0.3745
153
0.3693
2931
X-RAY DIFFRACTION
93
3.9317-3.9879
0.3461
164
0.36
2945
X-RAY DIFFRACTION
95
3.9879-4.0474
0.3835
137
0.3406
3004
X-RAY DIFFRACTION
95
4.0474-4.1106
0.3205
136
0.3181
3031
X-RAY DIFFRACTION
96
4.1106-4.1779
0.3014
146
0.316
3027
X-RAY DIFFRACTION
97
4.1779-4.2499
0.3075
171
0.3093
3073
X-RAY DIFFRACTION
99
4.2499-4.3272
0.3012
161
0.3016
3071
X-RAY DIFFRACTION
98
4.3272-4.4104
0.2846
177
0.3043
3072
X-RAY DIFFRACTION
99
4.4104-4.5003
0.3037
153
0.2884
3136
X-RAY DIFFRACTION
100
4.5003-4.5981
0.2407
156
0.2527
3147
X-RAY DIFFRACTION
100
4.5981-4.705
0.2638
150
0.2567
3118
X-RAY DIFFRACTION
100
4.705-4.8226
0.2715
154
0.2641
3165
X-RAY DIFFRACTION
100
4.8226-4.9528
0.2444
150
0.2805
3137
X-RAY DIFFRACTION
100
4.9528-5.0984
0.2736
174
0.2706
3135
X-RAY DIFFRACTION
100
5.0984-5.2628
0.3059
174
0.2798
3143
X-RAY DIFFRACTION
100
5.2628-5.4507
0.2881
168
0.2656
3152
X-RAY DIFFRACTION
100
5.4507-5.6686
0.367
179
0.298
3125
X-RAY DIFFRACTION
100
5.6686-5.9262
0.2955
186
0.3111
3122
X-RAY DIFFRACTION
100
5.9262-6.2381
0.3312
144
0.2913
3176
X-RAY DIFFRACTION
100
6.2381-6.6281
0.3188
177
0.2827
3180
X-RAY DIFFRACTION
100
6.6281-7.1385
0.2777
166
0.2719
3168
X-RAY DIFFRACTION
100
7.1385-7.8543
0.2449
152
0.2384
3201
X-RAY DIFFRACTION
100
7.8543-8.985
0.2164
195
0.1831
3211
X-RAY DIFFRACTION
100
8.985-11.298
0.1406
180
0.1445
3204
X-RAY DIFFRACTION
99
11.298-49.5936
0.2728
183
0.2236
3286
X-RAY DIFFRACTION
97
精密化 TLS
手法: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
3.8446
1.8099
0.6399
1.9884
-0.2557
3.2336
0.0888
0.5403
-0.1747
0.0804
-0.1207
0.1876
0.3288
0.1185
0.0406
1.036
0.1046
0.014
0.5485
-0.1301
1.1103
111.7838
-97.2765
-18.6797
2
7.3782
-0.6076
2.9413
2.8226
-2.3187
3.2556
-0.1437
1.3825
-0.5912
-0.1929
0.1689
-0.5421
0.8595
0.2028
0.0316
1.6074
-0.1378
0.067
1.4543
-0.6021
1.4678
105.2919
-114.4039
-37.6659
3
3.381
-0.6878
2.0639
6.1414
-5.5602
5.1944
0.3852
1.9947
0.3165
-1.6625
-0.0267
0.1876
3.2327
2.226
-0.3113
2.6143
0.3994
-0.1679
2.642
-0.955
2.048
101.1829
-112.8683
-66.2791
4
5.6024
-0.3003
0.5112
0.0583
-0.9487
3.8022
0.2523
0.2602
-0.5715
-0.2294
-0.1302
-0.0019
0.3179
-0.3072
-0.0588
1.1523
-0.011
-0.0548
0.4292
-0.2632
1.3722
72.0225
-110.3756
-17.3331
5
5.2412
-1.7297
-0.2595
4.9498
-2.1073
4.0619
0.3945
1.1614
-0.8984
0.3003
-0.3189
0.233
0.8571
-1.2901
-0.0653
1.4456
-0.093
-0.2005
1.7208
-0.4534
1.3795
55.6993
-118.594
-36.2652
6
1.6834
1.314
-0.4611
5.5346
-4.4136
4.5302
-1.0115
0.502
1.1334
-1.6429
-0.8501
-0.1626
2.8863
-2.0464
1.7023
3.257
0.1102
-0.2355
2.8377
-0.5883
2.1499
56.3263
-112.984
-64.6773
7
2.7983
-2.6262
0.1812
3.3017
-0.64
3.7765
0.1995
0.097
-0.1113
-0.3818
-0.1526
-0.2057
-0.0497
-0.2351
-0.0433
0.9455
-0.0321
-0.0287
0.5936
-0.1702
1.0496
34.3401
-91.9127
-16.0623
8
6.0009
-0.1585
-1.9433
5.7026
-4.3289
4.3064
0.4392
0.3483
-0.0875
-0.6084
-0.0857
-0.0275
-0.2937
-0.7445
-0.3981
1.6081
0.2593
-0.2183
1.1338
-0.3943
1.135
16.3014
-86.0963
-34.5288
9
3.6383
1.4128
-0.8434
6.2001
-1.5871
3.8164
-1.0248
1.0774
0.8834
-3.8987
1.7656
-0.4509
2.2803
-0.8457
-0.7191
3.5803
-0.1911
-0.2931
2.1603
0.0928
1.597
15.3495
-79.7065
-62.9258
10
1.9528
0.4826
-0.5779
4.2716
-0.8294
3.3962
-0.1677
0.2701
-0.0187
-0.2083
0.3481
-0.2443
0.1028
0.0999
-0.176
0.6363
-0.0398
0.0151
0.6004
-0.0696
0.6699
20.9677
-52.2526
-15.3931
11
8.8092
2.0051
-2.5322
6.7091
-2.3296
6.0166
-0.2049
1.0173
-0.0562
-0.9437
0.0783
-0.2815
-0.3031
0.6402
0.1327
1.2272
-0.1409
-0.0873
1.2277
0.1506
0.8744
11.8485
-36.2766
-34.3512
12
5.1054
1.4071
-1.7952
4.0296
-0.235
5.1225
-0.574
2.8701
-0.6705
-1.7079
0.8895
-0.7287
-0.5193
-1.7045
-0.4628
2.2939
-0.2051
0.0588
3.3292
0.2542
1.9795
13.8383
-34.4977
-63.2493
13
3.8024
1.3851
-1.315
1.7289
0.5226
3.6919
0.051
0.5943
0.3176
-0.1085
0.043
-0.166
-0.3018
-0.0989
-0.0834
0.7714
0.0596
-0.0171
0.629
0.1598
0.994
39.8054
-14.8508
-16.0974
14
5.7144
-0.5737
-2.8765
3.8368
0.6496
4.2716
-0.0471
1.0978
0.7136
-0.1346
0.1877
0.1938
-0.6929
-0.2674
-0.1775
1.3146
-0.0467
-0.0489
1.5389
0.6241
1.3723
44.9051
2.3785
-35.3562
15
2.5086
0.8901
-2.1587
3.2474
1.8489
3.8693
0.3961
0.4427
-0.3255
-0.1998
0.6571
0.0995
-0.9594
-2.8739
-1.1062
1.857
-0.0598
-0.0941
2.4907
1.1136
1.8389
47.85
1.581
-64.261
16
4.2258
-0.8379
-0.6207
0.9908
0.8726
3.641
0.2563
0.4006
0.8411
-0.1499
-0.2379
-0.0012
-0.2881
0.2426
0.0095
0.9366
-0.0726
0.0054
0.5964
0.2648
1.5263
79.472
-1.5368
-17.5998
17
4.2309
0.3968
0.6382
4.249
1.4118
4.6291
0.3021
1.5861
1.4325
-0.2345
-0.0981
0.32
-0.5076
1.1881
-0.2009
1.2593
-0.1004
0.0555
1.8987
0.7693
1.5988
94.4052
6.6552
-37.66
18
2.9011
1.7291
0.1048
5.5009
3.8203
3.3623
-0.7097
1.551
-0.8923
-2.8692
0.4272
0.1401
-1.5827
0.6812
0.375
3.0437
-0.0422
0.2283
2.9232
0.4546
2.1493
92.6787
2.285
-66.4916
19
3.9728
-2.2421
-0.5383
3.1968
0.9298
4.0717
0.1808
0.244
0.2573
-0.3152
-0.0706
0.1764
0.0139
0.3062
-0.0994
0.7177
-0.029
0.0082
0.5517
0.1968
0.9195
116.9893
-20.2395
-18.9784
20
7.0436
0.8571
1.1807
6.3949
3.8703
3.8714
0.1253
0.0645
-0.3879
-0.692
-0.18
0.1454
1.1821
0.8276
0.0475
1.56
0.2576
0.1217
1.2008
0.3442
0.9815
133.9082
-26.2367
-38.4851
21
5.1896
2.8574
0.5322
4.5916
1.8431
3.7092
-1.9378
1.6
-0.7221
-3.3612
1.4863
0.1003
0.133
0.7374
0.3229
3.3634
-0.2612
0.2
1.8353
0.0163
1.3774
132.0926
-31.6203
-66.7996
22
1.9206
0.3702
0.9388
4.5384
0.7027
3.3692
-0.084
0.3484
-0.0583
-0.174
0.2067
0.3568
0.0751
-0.0324
-0.1537
0.7206
0.0199
0.0039
0.6391
0.0558
0.7215
130.5352
-59.8322
-19.4051
23
7.2264
1.5853
0.9553
4.5349
-1.2037
2.2329
-0.0598
0.4984
-0.0699
-0.7874
0.3632
0.1015
0.2149
-0.2295
-0.2481
1.4915
-0.0338
0.0479
1.145
-0.263
0.9012
138.5102
-75.6377
-39.0339
24
5.9387
-0.023
2.3894
3.9494
0.2105
2.7165
-0.703
3.3978
0.2548
-1.5978
0.8166
1.1608
0.304
1.2031
-0.115
3.0701
-0.4923
-0.085
3.3643
-0.2756
1.7392
134.5506
-77.2244
-67.6809
精密化 TLSグループ
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid19orresid20orresid21orresid22orresid23orresid24orresid25orresid26orresid27orresid28orresid29orresid30orresid31orresid32orresid33orresid34orresid35orresid36orresid37orresid38orresid39orresid40orresid41orresid42orresid43orresid44orresid45orresid46orresid47orresid48orresid49orresid50orresid51orresid52orresid53orresid54orresid55orresid56orresid57orresid58