- PDB-5w79: Crystal Structure of the Group II Chaperonin from Methanococcus M... -
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Basic information
Entry
Database: PDB / ID: 5w79
Title
Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis, Cysteine-less mutant in the Apo State
Components
Chaperonin
Keywords
CHAPERONE / chaperonin / atpase
Function / homology
Function and homology information
chaperonin-containing T-complex / ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97945 Å / Relative weight: 1
Reflection
Resolution: 3.12→94.85 Å / Num. obs: 96473 / % possible obs: 99.1 % / Redundancy: 6.7 % / CC1/2: 0.994 / Net I/σ(I): 9.5
Reflection shell
Resolution: 3.12→3.29 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 13999 / CC1/2: 0.528 / % possible all: 100
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Processing
Software
Name
Classification
iMOSFLM
dataprocessing
SCALA
datareduction
PHASER
phasing
PHENIX
refinement
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.122→81.239 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.18
Rfactor
Num. reflection
% reflection
Rfree
0.2815
4942
5.13 %
Rwork
0.2491
-
-
obs
0.2508
96361
98.96 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 3.122→81.239 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
31096
0
40
7
31143
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
31327
X-RAY DIFFRACTION
f_angle_d
0.98
42144
X-RAY DIFFRACTION
f_dihedral_angle_d
10.028
19664
X-RAY DIFFRACTION
f_chiral_restr
0.084
5136
X-RAY DIFFRACTION
f_plane_restr
0.006
5440
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.122-3.1575
0.3948
167
0.3543
2983
X-RAY DIFFRACTION
100
3.1575-3.1946
0.3993
168
0.334
3062
X-RAY DIFFRACTION
100
3.1946-3.2336
0.3612
151
0.3278
3034
X-RAY DIFFRACTION
100
3.2336-3.2745
0.3553
154
0.3276
3065
X-RAY DIFFRACTION
100
3.2745-3.3176
0.3742
164
0.3173
3057
X-RAY DIFFRACTION
100
3.3176-3.3631
0.3362
191
0.3119
2991
X-RAY DIFFRACTION
100
3.3631-3.4111
0.3609
222
0.316
3010
X-RAY DIFFRACTION
100
3.4111-3.462
0.3378
145
0.2996
3034
X-RAY DIFFRACTION
100
3.462-3.5161
0.3454
166
0.2895
3043
X-RAY DIFFRACTION
100
3.5161-3.5738
0.3564
145
0.2929
2951
X-RAY DIFFRACTION
95
3.5738-3.6354
0.2937
123
0.2791
2946
X-RAY DIFFRACTION
96
3.6354-3.7015
0.2843
193
0.2649
2993
X-RAY DIFFRACTION
100
3.7015-3.7727
0.3002
145
0.2653
3074
X-RAY DIFFRACTION
100
3.7727-3.8497
0.3234
173
0.2872
3087
X-RAY DIFFRACTION
100
3.8497-3.9334
0.3304
133
0.2671
3078
X-RAY DIFFRACTION
100
3.9334-4.0249
0.3099
182
0.2661
3001
X-RAY DIFFRACTION
100
4.0249-4.1256
0.294
141
0.2594
3093
X-RAY DIFFRACTION
100
4.1256-4.2371
0.2478
149
0.2525
3053
X-RAY DIFFRACTION
100
4.2371-4.3618
0.2975
172
0.2465
3064
X-RAY DIFFRACTION
100
4.3618-4.5025
0.2522
165
0.2314
2873
X-RAY DIFFRACTION
93
4.5025-4.6635
0.2772
167
0.2212
3084
X-RAY DIFFRACTION
100
4.6635-4.8501
0.2404
185
0.2273
3044
X-RAY DIFFRACTION
100
4.8501-5.0709
0.2541
160
0.2261
3043
X-RAY DIFFRACTION
99
5.0709-5.3382
0.2896
177
0.2349
3124
X-RAY DIFFRACTION
100
5.3382-5.6725
0.3154
190
0.2472
3048
X-RAY DIFFRACTION
100
5.6725-6.1104
0.2741
146
0.2547
3000
X-RAY DIFFRACTION
96
6.1104-6.725
0.2939
134
0.2476
3152
X-RAY DIFFRACTION
100
6.725-7.6975
0.2253
204
0.2051
3114
X-RAY DIFFRACTION
100
7.6975-9.6955
0.1879
154
0.1629
3088
X-RAY DIFFRACTION
96
9.6955-81.2668
0.2074
176
0.2115
3230
X-RAY DIFFRACTION
96
Refinement TLS params.
Method: 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
2.7598
0.4209
-0.1167
1.2522
0.0565
1.6591
0.0027
-0.1984
0.0016
-0.0379
0.0641
0.1423
0.1499
-0.0984
0.0001
0.6047
-0.0602
0.0279
0.4001
0.0054
0.5102
-104.7165
-5.2355
4.776
2
2.4156
-0.2175
1.8694
2.6939
1.2311
2.6431
-0.0195
-0.3723
0.4463
0.4396
-0.0911
0.1419
-0.1042
0.5241
-0
0.7423
0.0341
0.0011
0.655
0.0034
0.7662
-83.8605
-4.582
21.991
3
1.3014
-0.5213
-0.5908
2.2383
0.964
1.2532
-0.1161
0.0937
-0.0498
0.345
0.2853
0.3474
0.2859
0.0124
-0
1.1862
0.0277
-0.0507
1.0033
-0.0962
0.9188
-86.6796
10.9204
50.7664
4
2.0094
0.6763
-0.2611
3.0608
0.5073
1.9836
0.081
-0.1368
-0.2163
0.167
-0.0277
-0.0443
0.2329
0.0156
-0.0002
0.5536
-0.0142
-0.0065
0.4344
0.005
0.5449
-74.4672
21.3895
1.3889
5
2.8374
0.9111
-0.3695
2.6126
2.8349
3.0256
0.067
-0.6032
0.1827
0.2384
-0.0942
-0.1306
-0.4047
0.1308
0
0.8357
-0.0488
-0.0135
0.8301
-0.0738
0.7956
-59.9841
32.6406
21.3289
6
1.4659
-0.7802
-0.3594
1.9149
0.9316
1.9329
-0.2638
0.105
-0.2529
-0.0765
0.2188
0.0704
-0.0037
0.3676
-0
1.1063
-0.059
-0.1035
1.0484
-0.1711
0.9355
-74.2377
36.4504
50.9845
7
2.1799
-0.9624
-0.7235
2.6789
0.1039
1.795
-0.0668
-0.0215
-0.0766
0.1733
0.0327
-0.2582
0.1389
0.2388
-0.0023
0.487
-0.0312
-0.0658
0.5011
-0.0316
0.5586
-70.9077
61.6788
5.72
8
2.4549
1.3018
-2.4308
2.0436
-0.1688
3.8001
-0.228
-0.1023
0.0359
0.5532
0.3417
-0.2567
-0.3188
0.1066
0.001
0.7829
-0.035
-0.2346
0.7068
-0.1553
0.7806
-69.1043
75.9226
28.6355
9
2.3312
1.281
-0.9055
3.3213
-0.5568
1.3008
-0.1126
0.0428
-0.2154
-0.2516
0.1939
0.1471
-0.0705
-0.0755
-0
0.9681
0.0222
-0.1983
0.838
-0.0786
0.7035
-83.3475
63.3431
55.7533
10
2.9929
-0.541
-0.9752
2.1586
0.0692
1.9721
0.0321
-0.1085
0.0119
0.1012
0.0109
-0.2245
0.0028
0.2079
-0.0002
0.511
-0.0557
-0.0908
0.444
-0.01
0.4595
-96.4785
91.7299
15.1757
11
2.4766
1.7552
-2.6307
1.6324
-1.1185
3.6842
0.1604
-0.3101
-0.3388
0.4462
-0.1221
0.0129
-0.3176
-0.0689
-0
0.8476
0.0326
-0.05
0.6335
-0.0638
0.7066
-105.7321
98.9862
39.5445
12
1.2008
0.1435
-0.6784
3.4487
-1.5382
1.9838
0.1387
0.1735
-0.1254
0.2978
-0.1852
-0.1004
-0.1498
-0.2083
-0
0.9807
-0.0671
-0.0685
0.8661
0.0383
0.7492
-107.9281
75.7326
62.8395
13
3.3003
0.2608
-0.2396
2.3074
-0.201
1.0388
-0.0273
-0.1261
0.0401
0.1088
-0.011
-0.1548
-0.0978
0.1392
-0.0003
0.558
-0.0333
-0.0275
0.4201
0.0163
0.5358
-135.8767
93.8681
24.1007
14
1.9772
-0.7111
-0.5669
2.9517
-2.1084
2.5654
-0.5291
-0.2099
-0.2683
0.6877
0.3079
0.0549
0.4927
-0.0123
-0
1.0672
0.0182
0.178
0.8939
-0.0069
0.66
-147.8465
88.3061
47.6585
15
3.1612
-3.1712
0.0903
1.9439
-0.7118
2.0138
0.319
-0.0217
0.1883
-0.2221
0.0909
-0.3629
-0.2509
-0.0342
0
1.158
-0.0264
0.1588
0.9
0.0303
0.956
-133.6354
66.154
67.868
16
2.3593
0.328
-0.1546
3.3011
-0.2055
1.2729
0.0806
-0.2656
0.1401
0.2619
-0.0298
0.0524
-0.2365
-0.0181
-0.0003
0.6181
-0.0284
0.0748
0.4831
0.0077
0.5289
-166.2014
67.0033
27.2134
17
2.2057
-1.733
0.9515
2.6875
-2.2907
1.8573
-0.2847
-0.3052
-0.0985
0.4052
0.0827
-0.0396
0.4861
-0.0407
0.0001
0.932
-0.0706
0.2189
0.7469
-0.0067
0.6381
-171.6342
50.4602
47.9224
18
3.8479
-0.9866
1.2438
2.3061
-0.2329
1.3381
0.1576
0.0576
0.0795
-0.0277
0.1154
-0.2375
0.0122
0.1008
-0
0.994
0.0721
0.1638
0.7561
-0.0072
0.5795
-146.5811
40.1304
67.0919
19
1.4891
-0.6412
0.0756
3.2023
0.5393
1.3495
-0.0167
-0.1466
0.0774
0.3107
0.0889
0.3263
-0.1432
-0.1649
-0.0008
0.6459
-0.0787
0.087
0.5425
0.0283
0.5597
-169.7878
26.7642
22.8061
20
3.1499
0.6137
1.5019
1.837
0.3006
0.8784
-0.019
-0.3919
-0.2925
0.4319
0.056
-0.0648
0.2637
-0.0246
-0
0.9984
-0.0452
0.1094
0.7061
0.1627
0.7377
-163.078
7.2656
40.4392
21
4.6413
0.8918
0.8998
1.3129
0.6211
1.7222
0.2542
-0.3475
0.1968
-0.2124
0.0552
-0.038
0.1352
-0.1101
-0
1.1821
0.0449
-0.0292
0.8393
0.0288
0.7127
-138.5452
13.4154
61.7563
22
3.3213
-0.5275
-0.1468
1.6109
0.5417
1.345
-0.011
-0.2173
-0.0371
0.0931
0.1217
0.1201
-0.0641
-0.1092
0
0.6004
-0.1282
0.0097
0.4479
0.0493
0.4803
-144.126
-3.3251
13.6856
23
2.6968
1.0509
2.3581
1.4607
0.4407
2.3846
0.0956
-0.3004
-0.0309
0.3376
0.0111
-0.0927
0.0044
0.3244
-0
1.0206
0.0071
-0.0503
0.6689
0.0558
0.6755
-125.9593
-15.5749
29.5933
24
1.1126
0.3434
0.8334
3.0769
0.8795
1.6884
0.2782
0.0458
0.163
0.126
-0.17
0.2367
-0.0627
-0.0224
0
1.1008
-0.0344
0.0075
0.9359
-0.0768
0.788
-113.0971
1.2468
54.7929
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid8orresid9orresid10orresid11orresid12orresid13orresid14orresid15orresid16orresid17orresid18orresid19orresid20orresid21orresid22orresid23orresid24orresid25orresid26orresid27orresid28orresid29orresid30orresid31orresid32orresid33orresid34orresid35orresid36orresid37orresid38orresid39orresid40orresid41orresid42orresid43orresid44orresid45orresid46orresid47