- PDB-3rb8: Structure of the phage tubulin PhuZ(SeMet)-GDP -
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Open data
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Basic information
Entry
Database: PDB / ID: 3rb8
Title
Structure of the phage tubulin PhuZ(SeMet)-GDP
Components
Putative uncharacterized protein
Keywords
UNKNOWN FUNCTION / Tubulin
Function / homology
Function and homology information
establishment of localization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / host cell cytoplasm / GTPase activity / GTP binding / identical protein binding Similarity search - Function
Method to determine structure: MAD / Resolution: 2.6→46.379 Å / SU ML: 0.34 Isotropic thermal model: Isotropic with TLS refinement with eleven groups σ(F): 1 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2373
1867
9.92 %
random
Rwork
0.1633
-
-
-
obs
0.1706
18830
95.32 %
-
all
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23023
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-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.427 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-5.2866 Å2
-0 Å2
0 Å2
2-
-
-3.2448 Å2
-0 Å2
3-
-
-
8.5313 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→46.379 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2419
0
29
14
2462
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
2487
X-RAY DIFFRACTION
f_angle_d
1.141
3385
X-RAY DIFFRACTION
f_dihedral_angle_d
14.645
922
X-RAY DIFFRACTION
f_chiral_restr
0.07
404
X-RAY DIFFRACTION
f_plane_restr
0.004
435
LS refinement shell
Refine-ID: X-RAY DIFFRACTION
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection obs
% reflection obs (%)
2.6-2.6705
0.3415
123
0.2491
1181
1181
85
2.6705-2.749
0.3643
134
0.2537
1203
1203
88
2.749-2.8377
0.3505
133
0.2336
1223
1223
90
2.8377-2.9392
0.3427
138
0.2158
1253
1253
91
2.9392-3.0568
0.2815
136
0.2125
1271
1271
94
3.0568-3.1959
0.3134
147
0.2061
1332
1332
97
3.1959-3.3643
0.324
151
0.1935
1360
1360
99
3.3643-3.5751
0.249
154
0.1838
1346
1346
98
3.5751-3.851
0.2044
157
0.15
1329
1329
99
3.851-4.2383
0.2244
141
0.1345
1376
1376
99
4.2383-4.851
0.1678
150
0.1095
1348
1348
100
4.851-6.1095
0.1969
147
0.1451
1378
1378
100
6.1095-46.3864
0.2029
156
0.1487
1363
1363
100
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
0.4376
-0.1173
0.1835
0.2989
0.0534
0.3723
-0.2409
-0.0226
0.0966
0.375
0.0152
-0.2567
-0.4987
0.1391
-0.0396
0.6371
0.0575
-0.3866
0.2404
-0.0387
0.6271
4.4315
4.7768
-1.7166
2
0.2574
0.1223
-0.4037
0.9652
-0.9981
1.3724
-0.6739
0.0922
1.0339
-0.1421
-0.2885
-0.2168
-0.8433
0.1541
-0.3363
1.0642
0.1336
-0.6223
0.6127
-0.1859
1.0126
15.3378
1.2578
2.774
3
0.3878
-0.1716
0.1849
1.2592
-0.6157
0.3549
-0.1435
-0.3146
0.1726
0.7655
0.3376
-0.1374
-0.3441
-0.083
0.0542
0.6524
0.1498
-0.1345
0.4547
0.0115
0.337
5.8419
-7.5469
0.4418
4
1.1826
-0.1424
0.3951
1.3256
0.3443
0.3878
-0.0761
0.1502
0.052
0.4865
0.1355
-0.011
0.3279
0.097
-0.0291
0.3654
0.0489
-0.0838
0.2277
0.0166
0.2402
5.6162
-10.2373
-9.1494
5
0.0576
0.1788
0.0959
0.9841
-0.3975
1.3251
-0.2244
-0.142
0.0535
-0.0748
-0.0012
-0.3685
0.0384
0.1337
0.1099
0.4147
-0.0609
0.0416
0.4572
0.0634
0.3691
4.4398
-4.8005
-16.0528
6
0.0472
-0.2227
0.0754
1.0535
-0.3535
0.3613
-0.1019
-0.0518
0.2332
0.0428
-0.1802
-0.7389
-0.1497
0.2202
-0.3389
0.8194
-0.0155
-0.4026
-0.0133
0.1721
0.6451
3.3084
7.4044
-13.46
7
0.3312
-0.1326
0.3471
1.5603
0.4785
0.633
0.0613
-0.4202
-0.1868
-0.1545
-0.1649
1.0436
0.0081
-0.4157
0.063
0.3522
-0.0259
0.0556
0.6025
0.0397
0.6554
-12.403
-4.6901
-12.2029
8
0.5
-0.0394
-0.4166
0.9815
-0.1673
0.4134
-0.7129
0.4377
0.3982
-0.7006
-0.2493
0.088
-0.7716
0.1361
-1.1284
0.5746
0.0381
-0.6264
0.3561
0.1298
0.6366
-12.1523
3.536
-23.9418
9
1.3228
-0.51
-0.5542
1.2904
-0.341
0.5104
-0.4024
-0.0795
0.4734
-0.3468
0.0751
0.5228
-0.575
-0.5213
-0.5398
0.4966
0.1734
-0.2825
0.4976
-0.0677
0.6915
-13.2321
5.7334
-18.2082
10
0.4177
0.0838
-0.4826
0.9921
0.3668
1.5117
-0.3794
0.4884
0.1639
-0.1978
0.2387
-0.5352
-0.0032
0.2427
0.0568
0.4508
-0.1126
0.0226
0.6621
-0.0905
0.4001
15.431
-13.4639
-24.709
11
2.3849
-1.1648
-0.1854
2.991
0.1304
0.5958
-0.1396
0.3501
-0.5466
0.9078
0.1846
0.5487
0.439
-0.1196
0.0286
0.5422
-0.0496
-0.0752
0.5183
0.0672
0.5026
49.9479
-20.4309
-13.0733
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAAND (RESSEQ2:32)
2
X-RAY DIFFRACTION
2
CHAINAAND (RESSEQ33:59)
3
X-RAY DIFFRACTION
3
CHAINAAND (RESSEQ60:94)
4
X-RAY DIFFRACTION
4
CHAINAAND (RESSEQ95:143)
5
X-RAY DIFFRACTION
5
CHAINAAND (RESSEQ144:160)
6
X-RAY DIFFRACTION
6
CHAINAAND (RESSEQ161:178)
7
X-RAY DIFFRACTION
7
CHAINAAND (RESSEQ179:214)
8
X-RAY DIFFRACTION
8
CHAINAAND (RESSEQ215:238)
9
X-RAY DIFFRACTION
9
CHAINAAND (RESSEQ239:271)
10
X-RAY DIFFRACTION
10
CHAINAAND (RESSEQ272:294)
11
X-RAY DIFFRACTION
11
CHAINAAND (RESSEQ295:315)
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