- PDB-3mqo: The Crystal Structure of the PAS domain in complex with isopropan... -
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Basic information
Entry
Database: PDB / ID: 3mqo
Title
The Crystal Structure of the PAS domain in complex with isopropanol of a Transcriptional Regulator in the LuxR family from Burkholderia thailandensis to 1.7A
Components
Transcriptional regulator, LuxR family
Keywords
Transcription regulator / PAS DOMAIN / LuxR / regulator / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Resolution: 1.7→50 Å / Num. obs: 29569 / % possible obs: 97.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Χ2: 1.854 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.7-1.76
3.7
0.458
2872
0.638
1
96.3
1.76-1.83
3.8
0.334
2897
0.689
1
96.6
1.83-1.91
3.8
0.253
2938
0.911
1
96.8
1.91-2.02
3.8
0.179
2911
1.045
1
97
2.02-2.14
3.8
0.136
2944
1.577
1
97.4
2.14-2.31
3.8
0.105
2974
1.632
1
97.5
2.31-2.54
3.8
0.085
2974
1.83
1
98
2.54-2.91
3.8
0.071
2996
2.51
1
98.3
2.91-3.66
3.7
0.056
3023
2.918
1
98.5
3.66-50
3.5
0.056
3040
4.936
1
95.9
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.004
dataextraction
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
HKL-3000
phasing
SHELX
phasing
MLPHARE
phasing
DM
phasing
ARP/wARP
modelbuilding
Coot
modelbuilding
Refinement
Resolution: 1.7→31.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.239 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.241
1483
5 %
RANDOM
Rwork
0.225
-
-
-
obs
0.226
29569
97.2 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 25.929 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.05 Å2
0 Å2
-0.06 Å2
2-
-
-0.06 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→31.54 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1797
0
30
87
1914
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
1885
X-RAY DIFFRACTION
r_angle_refined_deg
1.221
1.959
2556
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.717
5
241
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
26.885
21.954
87
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.145
15
298
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.293
15
21
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
285
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
1437
X-RAY DIFFRACTION
r_mcbond_it
0.458
1.5
1164
X-RAY DIFFRACTION
r_mcangle_it
0.71
2
1868
X-RAY DIFFRACTION
r_scbond_it
1.6
3
721
X-RAY DIFFRACTION
r_scangle_it
2.152
4.5
682
LS refinement shell
Resolution: 1.701→1.745 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.332
112
-
Rwork
0.29
1972
-
all
-
2084
-
obs
-
-
95.68 %
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
10.7668
-1.8607
-0.0691
18.0186
7.1386
-4.8302
0.0114
-0.1864
-0.0579
-0.0345
-0.0986
0.6938
0.3
-0.2846
0.0872
0.1258
-0.0387
0.0138
0.3726
0.0362
0.1506
6.3146
18.0069
19.4761
2
17.6571
6.0077
-0.5855
17.2229
2.2851
0.131
-0.2925
-0.1849
-0.2567
-0.4873
0.1788
0.5958
0.1356
-0.2912
0.1137
0.0756
-0.0425
-0.0378
0.2293
0.0265
0.0247
15.6176
16.6064
17.097
3
10.1815
6.228
7.3854
8.6018
5.7405
9.4767
-0.1655
-0.6424
0.4464
0.151
-0.0299
0.3228
-0.3191
-0.4555
0.1955
0.04
0.0315
0.0081
0.1638
-0.0153
0.0423
20.3591
26.0302
26.3275
4
8.2538
7.4424
1.0516
11.3077
1.2024
1.8574
-0.0488
-0.2764
0.6634
0.2491
-0.0494
0.3579
-0.1025
-0.2338
0.0983
0.0937
0.0272
-0.0014
0.1853
-0.0247
0.0249
22.9223
24.3512
28.4909
5
7.837
-5.9631
-0.9785
9.3855
1.3884
6.4784
-0.0311
-0.0478
-0.3906
0.0114
-0.1025
-0.3442
0.4902
-0.0104
0.1336
0.0788
-0.0186
0.0265
0.0912
0.0166
0.0745
20.8692
14.3773
21.0853
6
9.4118
1.5347
-0.5246
4.9708
-8.5909
11.0992
-0.1105
0.0577
-0.6742
-0.0416
-0.0024
-0.1221
0.3601
0.1784
0.1129
0.128
0.0202
0.0283
0.0517
0.0206
0.2129
28.0604
11.9922
20.644
7
1.9904
3.4614
-3.0777
35.9107
16.6486
11.7044
-0.1753
-0.133
-0.3367
0.6695
0.1762
-0.5599
0.7012
-0.3193
-0.0009
0.1337
-0.0209
-0.0214
0.1814
0.0569
0.1022
23.4886
14.6671
29.817
8
1.554
3.2088
0.9755
1.6888
-1.3991
12.4405
-0.0885
-0.1723
-0.1093
-0.0303
-0.231
-0.2812
0.2329
0.3378
0.3195
0.0748
-0.0051
0.0043
0.1276
0.0198
0.1005
30.2219
21.5352
28.6595
9
5.1495
2.9395
5.356
13.7401
7.3763
5.2157
-0.0569
-0.0711
0.0828
0.539
0.0146
-0.4738
0.2307
0.1708
0.0423
0.0567
0.0153
0.0143
0.184
0.066
0.089
36.3192
22.5389
24.4075
10
13.8659
2.1545
-6.235
14.3917
-7.6703
8.5996
-0.0768
0.1092
0.2771
0.1639
0.1117
-0.1874
-0.144
0.6194
-0.035
0.056
-0.0191
-0.0284
0.2062
-0.0093
0.179
38.0744
28.5648
23.9505
11
18.2516
-15.0297
-2.141
14.9623
-5.6778
7.5409
-0.2185
-0.1924
0.9846
0.4572
-0.0567
-0.5646
-0.5824
0.3867
0.2752
0.1273
-0.0236
-0.0947
0.087
-0.0012
0.333
32.9687
33.8789
20.7196
12
3.0341
-8.3958
3.1605
14.6092
-0.7166
0.1582
-0.0405
0.2072
0.4302
0.1013
0.048
-1.0087
-0.0463
-0.1235
-0.0075
0.1804
0.0059
-0.0413
0.1475
0.011
0.3004
26.4767
39.3368
16.3778
13
2.4087
-5.9666
-2.449
9.449
3.2484
4.386
-0.1576
0.1475
0.089
0.0736
-0.0684
-0.0244
-0.1717
0.1579
0.226
0.055
-0.0108
0.0109
0.1311
0.0396
0.1478
27.6046
30.603
13.5179
14
2.09
0.7107
-0.4428
5.661
-5.8374
5.7979
0.088
-0.1333
-0.2915
0.8295
-0.4237
-0.3361
-0.3616
0.3539
0.3357
0.2453
0.0236
-0.0086
0.1385
0.0336
0.1532
34.5672
17.4186
19.4384
15
9.2332
-3.6846
3.4577
7.7659
-4.284
6.9777
0.0184
0.383
-0.6434
-0.107
-0.1637
-0.494
0.5159
0.3235
0.1454
0.0554
0.0393
0.0425
0.1669
-0.0114
0.167
35.7027
16.4344
15.565
16
9.08
-5.4808
-4.6469
9.3076
4.8029
5.5376
-0.0017
0.1509
0.0606
-0.19
-0.272
0.3355
-0.3531
-0.1513
0.2737
0.0417
0.008
-0.0091
0.0805
0.0131
0.057
22.0854
29.3678
16.6085
17
-0.8934
2.0524
-0.6006
16.933
-6.7513
1.7988
-0.0622
0.105
0.166
0.4186
0.1006
-0.238
-0.1998
-0.2258
-0.0384
0.1643
0.0436
-0.0891
0.1385
-0.0491
0.2317
22.5655
38.6914
23.1064
18
0.2261
2.7084
0.1203
1.0079
-2.9288
4.4763
-0.2315
-0.1573
0.2985
0.0736
-0.1642
0.1538
-0.3505
-0.0782
0.3957
0.0402
0.0348
-0.0198
0.1271
-0.0589
0.1083
21.389
28.2855
21.4215
19
10.2871
-0.0125
-1.0322
14.0483
0.6399
16.0782
-0.0572
0.7213
-0.4963
-0.4619
0.0433
-0.5167
0.8903
0.416
0.0139
0.05
0.0192
0.0272
0.1653
-0.0254
0.0741
28.1399
17.0551
12.1855
20
2.1093
2.5333
3.3477
3.4797
-1.0007
4.4341
-0.0966
-0.2098
0.2607
0.8679
0.1452
0.5849
-0.2028
-0.2374
-0.0486
0.2099
0.0594
0.0505
0.3623
-0.0246
0.1249
9.9289
26.2304
23.187
21
7.2328
4.346
-0.476
6.5817
-0.4828
14.8939
0.1
-0.3652
0.0765
0.195
0.1086
0.0286
-0.3635
-0.2704
-0.2086
0.0473
0.0171
-0.0002
0.1194
-0.0031
0.0861
13.2989
27.7757
15.2347
22
8.9011
4.0214
5.7112
6.1209
5.8588
8.6389
0.2147
-0.3874
-0.2766
0.1885
-0.2444
0.2338
0.385
-0.5216
0.0297
0.0374
-0.0176
0.0121
0.1272
0.0236
0.0714
6.4158
18.5477
8.589
23
3.9535
-0.2579
0.0614
12.5835
12.2603
16.804
-0.1157
-0.2631
-0.1415
0.4331
0.0058
0.55
0.741
-0.2843
0.1099
0.0232
-0.015
0.0067
0.1242
0.0484
0.0741
4.0567
19.6555
5.4522
24
6.0186
2.1074
-3.2761
1.5745
-5.8502
10.8067
0.2082
-0.1332
0.4557
-0.1134
0.0266
0.0257
-0.2449
-0.0855
-0.2348
0.0825
0.0095
0.036
0.0716
-0.0188
0.0949
11.0724
30.0343
8.6527
25
4.8223
-0.6668
-0.9337
5.3279
0.854
3.8768
0.0448
0.1487
0.2432
-0.2006
-0.0431
0.0403
-0.1068
-0.0486
-0.0017
0.1278
-0.0062
0.0142
0.0576
0.013
0.088
11.4551
32.0856
2.0267
26
15.775
4.6756
6.9961
31.2135
6.7384
-0.3919
-0.056
-0.3518
0.5826
0.3714
-0.1739
0.7389
-0.2138
-0.2806
0.2299
0.0519
0.0228
0.009
0.1388
-0.017
0.1086
2.9699
29.4539
5.936
27
10.8419
-4.831
2.2206
6.7258
3.5374
1.4422
0.2525
0.4048
-0.1978
-0.2396
-0.0738
-0.0489
0.0625
0.0969
-0.1788
0.05
-0.0086
-0.0012
0.1336
0.0004
0.0519
4.547
22.1212
-0.7099
28
5.5119
3.4717
-1.7616
10.6072
-0.5343
7.9529
-0.0379
0.3988
0.1029
-0.33
0.1858
0.4005
0.0095
-0.0817
-0.1479
0.0265
0.0208
0.0033
0.1374
0.0176
0.0734
10.0707
21.1963
-7.28
29
6.9601
-10.3403
-8.4499
15.8857
-1.3037
12.1292
-0.1199
0.7801
-0.4781
-0.247
0.0235
0.0464
0.1351
-0.3883
0.0963
0.134
-0.0029
0.0183
0.3
-0.0747
0.0681
11.7544
15.3125
-7.6307
30
9.4785
-9.6374
-0.3979
16.8897
-13.7465
27.5848
0.4241
0.4498
-0.2399
-0.0197
-0.1278
0.1676
0.9194
-0.2336
-0.2963
0.2877
0.0352
-0.0452
0.1563
-0.0655
0.1077
13.9075
10.1961
-2.8728
31
4.1335
-2.4516
7.2793
8.2711
-1.5075
4.9848
0.1902
0.0513
-0.0986
-0.2514
0.0201
0.1028
0.1956
0.5202
-0.2102
0.2209
0.0506
-0.0129
0.2317
0.0067
0.1518
16.8948
4.7539
4.3664
32
4.6687
1.4871
-2.819
6.9778
-6.1557
5.9087
0.3032
0.1224
-0.0526
0.0019
0.0054
0.2062
0.1539
0.3531
-0.3086
0.1062
0.0772
0.0037
0.2009
-0.0355
0.0797
19.7519
13.4719
4.1826
33
5.9586
-6.6407
-1.5767
5.362
2.0272
0.0631
0.0782
0.1579
-0.2962
-0.0798
-0.2228
0.5209
-0.0229
-0.0509
0.1446
0.132
0.005
0.0199
0.1874
-0.0038
0.0903
15.9387
25.381
-3.7857
34
8.6704
-3.2324
0.6672
3.7943
-0.3075
5.5445
0.0947
0.3332
0.5252
-0.309
-0.0198
-0.0235
-0.4234
0.1268
-0.0749
0.094
-0.0326
0.0285
0.1254
0.0106
0.0799
17.6179
28.6074
-4.6138
35
8.1696
5.0892
-3.5314
7.3569
-4.2206
4.1331
0.1015
-0.1667
-0.2311
0.0161
-0.1617
-0.1377
0.1833
0.0195
0.0602
0.0876
0.0162
0.0153
0.079
-0.0151
0.0319
14.6374
13.3704
8.903
36
2.056
-3.7836
5.3588
10.7705
-4.5574
3.9245
0.3765
0.0628
-0.2166
-0.5675
-0.213
0.4477
0.4318
0.1486
-0.1636
0.1926
-0.0143
-0.0246
0.1025
0.0199
0.1214
9.3076
6.0201
6.144
37
12.7492
4.8584
-0.8332
5.6695
1.8832
2.0608
0.2618
-0.2274
-0.0618
-0.0452
-0.1558
0.2656
0.2273
-0.0233
-0.106
0.1017
-0.0089
-0.0288
0.0759
0.0149
0.0661
11.5232
16.443
9.0307
38
15.7053
5.9578
-1.3625
13.7388
-3.9531
8.7863
-0.2601
0.4185
0.1884
-0.1525
0.1031
-0.2936
-0.1947
0.3475
0.157
0.0261
-0.004
0.0283
0.1286
0.0025
0.031
20.458
26.6828
3.7104
39
7.039
-11.6954
15.172
18.0851
-15.2853
30.969
-0.7292
0.5244
0.2657
0.2221
0.0597
0.3074
-0.8282
0.8823
0.6694
0.1284
-0.0581
0.1093
0.3604
0.0363
0.2712
31.6828
29.7099
7.2372
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
4 - 8
2
X-RAY DIFFRACTION
2
A
9 - 16
3
X-RAY DIFFRACTION
3
A
17 - 22
4
X-RAY DIFFRACTION
4
A
23 - 27
5
X-RAY DIFFRACTION
5
A
28 - 33
6
X-RAY DIFFRACTION
6
A
34 - 38
7
X-RAY DIFFRACTION
7
A
39 - 45
8
X-RAY DIFFRACTION
8
A
46 - 50
9
X-RAY DIFFRACTION
9
A
51 - 55
10
X-RAY DIFFRACTION
10
A
56 - 60
11
X-RAY DIFFRACTION
11
A
61 - 66
12
X-RAY DIFFRACTION
12
A
67 - 72
13
X-RAY DIFFRACTION
13
A
73 - 78
14
X-RAY DIFFRACTION
14
A
79 - 85
15
X-RAY DIFFRACTION
15
A
86 - 91
16
X-RAY DIFFRACTION
16
A
92 - 98
17
X-RAY DIFFRACTION
17
A
99 - 104
18
X-RAY DIFFRACTION
18
A
105 - 110
19
X-RAY DIFFRACTION
19
A
111 - 116
20
X-RAY DIFFRACTION
20
B
4 - 9
21
X-RAY DIFFRACTION
21
B
10 - 15
22
X-RAY DIFFRACTION
22
B
16 - 22
23
X-RAY DIFFRACTION
23
B
23 - 27
24
X-RAY DIFFRACTION
24
B
28 - 34
25
X-RAY DIFFRACTION
25
B
35 - 39
26
X-RAY DIFFRACTION
26
B
40 - 44
27
X-RAY DIFFRACTION
27
B
45 - 49
28
X-RAY DIFFRACTION
28
B
50 - 56
29
X-RAY DIFFRACTION
29
B
57 - 60
30
X-RAY DIFFRACTION
30
B
61 - 66
31
X-RAY DIFFRACTION
31
B
67 - 72
32
X-RAY DIFFRACTION
32
B
73 - 78
33
X-RAY DIFFRACTION
33
B
79 - 83
34
X-RAY DIFFRACTION
34
B
84 - 91
35
X-RAY DIFFRACTION
35
B
92 - 99
36
X-RAY DIFFRACTION
36
B
100 - 105
37
X-RAY DIFFRACTION
37
B
106 - 110
38
X-RAY DIFFRACTION
38
B
111 - 115
39
X-RAY DIFFRACTION
39
B
116 - 121
+
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