- PDB-3r4v: Structure of the phage tubulin PhuZ-GDP -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3r4v
Title
Structure of the phage tubulin PhuZ-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: MOLECULAR REPLACEMENT Starting model: SeMet model solved using MAD Resolution: 1.67→46.399 Å / SU ML: 0.26 Isotropic thermal model: Isotropic with TLS refinement with ten groups Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2316
1701
4.39 %
random
Rwork
0.1861
-
-
-
obs
0.1881
37046
98.34 %
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all
-
38747
-
-
Solvent computation
Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.62 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
0.3061 Å2
-0 Å2
-0 Å2
2-
-
-1.0888 Å2
0 Å2
3-
-
-
0.7827 Å2
Refinement step
Cycle: LAST / Resolution: 1.67→46.399 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2406
0
29
271
2706
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
2614
X-RAY DIFFRACTION
f_angle_d
1.064
3578
X-RAY DIFFRACTION
f_dihedral_angle_d
13.536
997
X-RAY DIFFRACTION
f_chiral_restr
0.069
423
X-RAY DIFFRACTION
f_plane_restr
0.004
468
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 (%)
1.67-1.7297
0.4219
149
0.4709
3238
3238
88
1.7297-1.799
0.4195
168
0.3867
3671
3671
99
1.799-1.8808
0.3202
171
0.285
3717
3717
100
1.8808-1.98
0.2586
167
0.2395
3657
3657
98
1.98-2.104
0.2685
169
0.1963
3696
3696
100
2.104-2.2665
0.2424
170
0.1908
3718
3718
99
2.2665-2.4946
0.2093
173
0.1672
3756
3756
100
2.4946-2.8555
0.2432
173
0.174
3769
3769
100
2.8555-3.5974
0.2359
176
0.1793
3830
3830
100
3.5974-46.4169
0.1826
182
0.1474
3966
3966
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
2.1173
-1.6127
-0.4964
1.3719
-0.0008
1.2566
-0.5299
-0.5204
-0.7444
0.6654
0.2147
0.2572
0.5587
-0.0094
0.2877
0.4061
0.0644
0.1687
0.1572
0.0839
0.3149
-3.2728
-5.5711
-2.195
2
1.269
-0.7904
-0.0574
0.9718
0.2137
0.5913
-0.6511
-0.4966
-0.959
0.9588
0.2319
0.8324
0.7162
-0.3121
0.4097
0.6195
0.0761
0.4029
0.2882
0.1488
0.5371
-12.6878
-4.155
3.2019
3
1.0859
-0.0127
-0.4967
1.1469
-0.1743
0.4257
-0.3677
-0.4997
-0.176
0.6794
0.2427
0.2723
-0.1846
-0.024
-0.0299
0.3896
0.1141
0.1145
0.2868
-0.0051
0.1536
-9.8185
10.0064
3.7476
4
1.3884
-0.681
-0.6266
1.8517
-0.1216
2.0255
-0.1628
0.061
-0.129
0.2936
0.1221
0.1639
-0.0467
-0.0486
0.0455
0.164
0.0043
0.0358
0.1051
-0.02
0.1158
-4.3186
8.7132
-9.443
5
3.1781
1.2224
0.4504
1.5334
1.8105
2.5907
-0.4281
0.5071
-0.948
-0.1014
-0.1082
0.6174
0.456
-0.3734
0.2161
0.3274
-0.106
0.0556
0.2453
-0.1837
0.4107
-10.5459
-5.8913
-18.0343
6
1.7218
-0.209
-1.2653
2.4274
-0.1533
1.5986
-0.2313
-0.0337
-0.0983
0.0459
0.0766
-0.4564
0.1954
0.3559
0.1128
0.1394
-0.0015
0.0102
0.2101
-0.0262
0.214
10.8746
2.6023
-15.3157
7
1.0284
-0.9498
-0.2366
1.732
-0.3287
1.7579
-0.524
-0.0022
-0.39
-0.1632
0.0965
-0.831
0.3687
0.2882
0.3389
0.239
0.0435
0.1985
0.2576
0.0253
0.5284
16.9502
-4.8295
-20.146
8
1.4675
-0.4069
-0.2405
2.0974
-0.6256
0.998
-0.61
-0.3769
-0.7336
0.0972
0.4498
0.1696
0.5448
0.2006
0.265
0.3625
0.1094
0.1909
0.2355
0.0576
0.4121
9.2149
-9.0946
-16.6464
9
0.7005
1.0905
-0.1259
1.9201
-0.409
1.1768
-0.1672
0.4701
0.3583
-0.0239
0.2308
0.3982
0.0099
-0.2414
-0.0883
0.1262
-0.0451
-0
0.2776
0.0411
0.1656
-15.1974
13.7919
-24.6332
10
1.5587
-0.1462
-0.3486
2.8373
-1.159
2.1234
0.1694
0.0555
0.4392
0.5422
0.0456
-0.1706
-0.4249
0.0258
-0.1989
0.2593
-0.0109
0.0394
0.1352
0.0008
0.175
-50.3636
21.0077
-12.4665
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAINAANDRESID2:28)
2
X-RAY DIFFRACTION
2
(CHAINAANDRESID29:51)
3
X-RAY DIFFRACTION
3
(CHAINAANDRESID52:80)
4
X-RAY DIFFRACTION
4
(CHAINAANDRESID81:156)
5
X-RAY DIFFRACTION
5
(CHAINAANDRESID157:171)
6
X-RAY DIFFRACTION
6
(CHAINAANDRESID172:228)
7
X-RAY DIFFRACTION
7
(CHAINAANDRESID229:255)
8
X-RAY DIFFRACTION
8
(CHAINAANDRESID256:270)
9
X-RAY DIFFRACTION
9
(CHAINAANDRESID271:294)
10
X-RAY DIFFRACTION
10
(CHAINAANDRESID295:315)
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