- PDB-4dz6: Transition state mimic of nucleoside-diphosphate kinase from borr... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4dz6
Title
Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and adp
Components
Nucleoside diphosphate kinase
Keywords
TRANSFERASE / SSGCID / NIAID / NUCLEOSIDE DIPHOSPHATE KINASE / KINASE / VANADATE / TRANSITION STATE MIMIC / TRANSITION STATE ANALOG / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information
nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
FOR CHAINS B, E AND F THE LIGANDS TENTATIVELY IDENTIFIED AS VO4 COULD NOT BE MODELED AS ADP OR ANY ...FOR CHAINS B, E AND F THE LIGANDS TENTATIVELY IDENTIFIED AS VO4 COULD NOT BE MODELED AS ADP OR ANY OTHER COMPONENT OF THE CRYSTALLIZATION DROP
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal grow
Temperature: 289 K / Method: vapor diffusion, sitting drop Details: EBS INTERNAL TRACKING NUMBER ACTIVATED SODIUM ORTHOVANADATE, 2 MM ADP, BOBUA.00664.A.A1_ PS00257 AT 17 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Resolution: 2.2→99.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.775 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.223
3003
5.1 %
RANDOM
Rwork
0.183
-
-
-
obs
0.185
59351
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 36.587 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.31 Å2
0 Å2
0 Å2
2-
-
-1.51 Å2
0 Å2
3-
-
-
1.2 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→99.47 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8065
0
116
328
8509
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.019
8394
X-RAY DIFFRACTION
r_angle_refined_deg
1.406
1.969
11366
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.808
5
1012
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.38
23.466
378
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.017
15
1459
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.85
15
53
X-RAY DIFFRACTION
r_chiral_restr
0.098
0.2
1252
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
6256
LS refinement shell
Resolution: 2.2→2.26 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.269
197
-
Rwork
0.234
3868
-
obs
-
-
99.73 %
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
2.591
-0.5373
-0.8508
0.5724
-0.0567
0.4371
-0.0019
-0.0847
-0.1482
0.0343
-0.0029
0.0755
-0.0109
0.0023
0.0048
0.0606
-0.0201
0.0201
0.0448
0.0106
0.034
19.2567
24.5661
22.8614
2
1.6444
0.3155
-0.5162
0.5991
-0.3648
1.3317
0.0175
-0.1475
-0.001
-0.0474
-0.0515
0.1113
0.104
0.013
0.0339
0.037
-0.0062
0.0235
0.0168
-0.013
0.0645
15.2907
21.9225
19.227
3
1.5023
0.252
-2.1866
1.2159
-1.161
3.7625
-0.1877
-0.2206
-0.0615
-0.0667
0.0174
-0.064
0.4005
0.2812
0.1704
0.2229
-0.0045
0.0614
0.0507
0.0247
0.0792
12.6293
10.9522
35.2347
4
1.1182
0.0271
-0.6004
0.4888
0.204
1.7054
-0.074
-0.1231
-0.1389
0.0865
0.0407
0.0487
0.058
0.208
0.0333
0.0574
0.0009
0.0373
0.034
0.008
0.0376
21.7083
24.7274
30.9548
5
1.1374
-0.0734
-1.1822
0.5605
-0.4929
2.2729
-0.0232
-0.0507
-0.1739
0.0092
0.0052
0.0935
0.2393
-0.0122
0.0179
0.1311
-0.0373
0.0014
0.0151
0.0067
0.1047
16.7072
16.0475
25.4715
6
6.9671
0.1967
2.5718
1.1995
0.2543
1.463
0.0107
0.1431
-0.0635
-0.1819
-0.0194
0.0067
0.0414
0.164
0.0087
0.0494
0.0102
0.0228
0.0761
-0.0196
0.0372
31.6643
25.7374
7.8783
7
2.712
0.1222
-0.7557
0.1549
0.3355
1.1897
-0.0215
0.0866
0.0403
-0.0141
-0.0336
0.0467
-0.0426
-0.0684
0.0551
0.0569
-0.007
0.015
0.0454
-0.0174
0.0671
9.8319
35.5175
13.5108
8
0.8325
0.0617
-0.2707
1.7163
0.0076
0.0885
0.0633
-0.0822
-0.0408
-0.14
-0.0772
0.0112
-0.023
0.0247
0.0139
0.0448
-0.0149
-0.029
0.0572
-0.0191
0.0569
7.4988
25.745
1.591
9
8.8769
-2.8466
5.1602
0.9408
-1.6447
4.1939
-0.0857
0.3923
0.1535
-0.0257
-0.065
-0.0127
-0.0581
0.3248
0.1507
0.1481
-0.0948
-0.0824
0.1302
0.0386
0.1136
8.398
33.2094
-7.7981
10
0.5907
-0.753
-0.9942
1.2563
1.1542
2.0668
-0.0451
0.1469
-0.0917
0.0877
-0.0864
0.2164
-0.0278
-0.1875
0.1315
0.0374
-0.0189
-0.0029
0.1112
-0.0094
0.0917
4.6814
36.5957
12.29
11
1.0834
0.7859
-0.4945
1.3267
0.4952
3.2162
-0.0598
0.1801
0.1841
-0.0477
0.0264
0.1256
-0.0664
-0.0678
0.0334
0.0452
-0.0034
-0.0064
0.0563
0.0429
0.0431
17.2447
43.7405
0.4832
12
0.6608
-0.1726
0.0198
0.5883
0.6813
2.8382
0.0168
0.0218
-0.0683
0.0103
-0.0373
0.2237
0.0431
-0.3091
0.0205
0.0134
-0.0234
0.0174
0.0713
-0.0083
0.1359
0.6921
31.897
15.0284
13
1.1358
-0.0085
0.2391
1.5352
1.2168
1.5777
0.0299
-0.0145
0.1159
-0.0035
0.02
-0.1041
0.0064
0.1396
-0.0499
0.0394
-0.0319
0.0278
0.0577
-0.0125
0.0766
39.5468
42.9728
19.7214
14
1.2729
0.2058
1.0849
3.3621
0.1112
0.9423
0.1276
0.2129
-0.1527
-0.3049
0.0155
-0.3775
0.0793
0.2296
-0.1431
0.0938
-0.0643
0.0595
0.1919
-0.0554
0.2322
51.9327
40.0471
10.8404
15
10.6425
-5.6233
6.3926
9.8926
-2.7059
3.9051
-0.2486
-0.0679
0.2882
0.9604
0.1544
-1.0568
-0.0708
-0.0333
0.0941
0.2039
-0.002
-0.0618
0.1724
-0.0446
0.1806
56.9051
25.3133
17.7845
16
0.7474
-0.0368
-0.2986
1.8642
0.2694
0.1727
0.0526
-0.1605
0.0405
0.0494
0.028
-0.306
-0.0191
0.1193
-0.0806
0.012
-0.0231
0.0194
0.1812
-0.0688
0.1471
46.9771
38.8084
18.2063
17
0.6643
-0.0592
-0.3156
1.2106
-0.0519
0.6197
0.0085
-0.0815
0.0636
0.1165
0.0364
-0.2161
0.0589
0.1935
-0.0448
0.0346
0.0039
-0.0069
0.1068
-0.0403
0.0981
44.7848
34.6321
19.3454
18
1.7189
-0.2371
-0.9416
2.5492
-2.4466
3.1699
0.1751
-0.3036
0.2475
0.2787
-0.1003
-0.1362
-0.4321
0.3541
-0.0748
0.1421
-0.1357
0.0244
0.1782
-0.1258
0.2421
40.3165
57.5574
32.0468
19
1.362
0.8299
0.1206
0.7552
-0.286
0.7587
0.1333
-0.0957
0.1131
0.2047
-0.0267
0.0634
-0.2316
-0.0542
-0.1065
0.1286
-0.0073
0.0838
0.0196
-0.0268
0.1203
12.6056
55.6988
31.2208
20
1.4916
-0.2861
0.2411
0.1566
0.0959
0.6548
0.0322
-0.1655
0.2015
0.0009
0.0679
-0.1093
-0.1595
-0.1363
-0.1
0.1927
0.0312
0.0965
0.0978
-0.055
0.1358
5.2424
59.0898
37.5351
21
23.381
-2.6101
1.1859
11.2368
-8.0416
5.9027
-0.0435
0.7813
0.0999
-0.0885
0.053
0.086
-0.1688
-0.1452
-0.0095
0.4754
0.0799
-0.0381
0.2891
-0.1112
0.0693
-9.7886
61.7414
28.3393
22
1.7895
0.0636
-0.3578
0.0696
0.1905
0.7288
0.0637
-0.1022
0.2143
-0.0239
-0.0475
0.0227
-0.1711
-0.1317
-0.0162
0.1688
0.0336
0.0732
0.0617
-0.056
0.1366
6.2193
58.2299
31.9851
23
1.2316
0.3318
0.1843
1.1825
0.8687
1.0611
0.0869
0.032
0.1693
-0.0509
-0.0861
0.2075
-0.1603
-0.1285
-0.0007
0.1055
0.0241
0.0729
0.0294
0.0003
0.1251
3.2186
55.4449
27.9158
24
2.3361
-0.8201
-2.7341
0.4721
0.3347
5.3662
0.0892
-0.0569
0.2141
0.0804
-0.0129
-0.1282
-0.4032
0.2091
-0.0763
0.2209
-0.0875
0.0683
0.0543
-0.0748
0.1972
27.3767
65.7666
31.5955
25
0.3448
0.1015
0.3485
0.6761
-0.2281
0.5603
-0.0422
0.0508
0.0723
-0.0232
0.0004
-0.0619
-0.0773
0.0671
0.0418
0.0778
-0.0448
0.0664
0.051
0.0015
0.1563
31.8131
54.0727
11.004
26
0.2999
-0.1218
0.1316
1.5829
0.0909
0.0975
0.0019
0.144
0.1171
0.0207
0.0149
-0.2386
-0.0544
0.0891
-0.0168
0.1522
-0.0571
0.0872
0.0985
0.025
0.1815
38.0663
59.3092
7.7489
27
5.0484
-3.4521
2.9901
7.9168
-3.1171
5.2055
-0.0217
0.2821
0.2742
0.3537
0.1612
0.2986
-0.2919
0.089
-0.1395
0.1616
-0.0468
0.1267
0.1055
0.0776
0.3118
33.0139
73.5688
8.2538
28
2.4649
0.9707
0.5016
1.48
0.7872
0.7265
0.0124
0.1253
0.284
-0.2909
-0.0175
-0.0782
-0.3371
0.0361
0.0052
0.2006
-0.0272
0.0452
0.0505
0.0282
0.1445
30.8921
54.4038
5.9623
29
1.3032
-0.6397
-0.6509
1.8196
0.6015
1.9798
0.0535
0.02
0.2545
-0.0735
0
-0.0228
-0.3267
0.0055
-0.0535
0.1488
-0.0392
0.0557
0.0236
0.0045
0.1603
27.968
63.3063
11.2206
30
4.5021
1.0463
1.765
1.8817
0.8948
0.8442
-0.0266
0.3165
0.0573
-0.2412
0.0798
-0.1423
-0.0974
0.1343
-0.0532
0.0762
-0.0204
0.074
0.0983
-0.0109
0.0804
33.3723
40.2308
0.0729
31
1.6891
1.2021
-0.8643
3.5359
-1.124
0.5482
0.0076
-0.218
0.02
0.3511
-0.0108
-0.064
-0.0963
0.0914
0.0032
0.1351
-0.0264
0.0149
0.0858
-0.0442
0.0318
23.4817
46.9147
41.1785
32
0.852
0.2957
-0.2202
0.7797
-0.1245
0.175
-0.008
-0.2642
0.0587
0.3529
0.0256
-0.0184
-0.0538
0.1533
-0.0176
0.2448
-0.0031
0.0217
0.2136
-0.0656
0.0432
23.5376
50.7664
48.5842
33
24.2518
-6.4838
4.4632
1.7431
-1.1946
0.8234
-0.3038
-1.1596
-2.201
0.1994
0.5187
0.5216
-0.1058
-0.1892
-0.2149
0.8043
0.1501
-0.353
0.5856
-0.0726
0.7017
40.5447
48.8459
56.9861
34
1.9684
0.0218
0.2302
1.3758
0.2575
0.1076
-0.105
-0.2564
0.0506
0.3626
0.1286
0.0009
0.0038
0.0715
-0.0236
0.2589
-0.0592
-0.0048
0.2238
-0.0742
0.0477
26.4852
47.2739
46.7506
35
1.1242
-0.516
-0.1877
0.5552
-0.6145
1.9549
0.0446
-0.2209
0.1523
0.119
0.0177
-0.1079
-0.1006
0.2236
-0.0623
0.1954
-0.0722
-0.0536
0.1236
-0.0722
0.1097
34.8383
45.4691
43.259
36
1.7003
0.2603
0.406
2.598
1.5421
1.5695
-0.0609
-0.2609
0.098
0.3349
-0.0531
0.3055
-0.0188
-0.1921
0.114
0.1645
0.0126
0.085
0.1073
-0.0129
0.0617
10.3832
41.764
45.593
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 29
2
X-RAY DIFFRACTION
2
A
30 - 47
3
X-RAY DIFFRACTION
3
A
48 - 75
4
X-RAY DIFFRACTION
4
A
76 - 122
5
X-RAY DIFFRACTION
5
A
123 - 157
6
X-RAY DIFFRACTION
6
A
158 - 169
7
X-RAY DIFFRACTION
7
B
2 - 35
8
X-RAY DIFFRACTION
8
B
36 - 55
9
X-RAY DIFFRACTION
9
B
56 - 77
10
X-RAY DIFFRACTION
10
B
78 - 95
11
X-RAY DIFFRACTION
11
B
96 - 131
12
X-RAY DIFFRACTION
12
B
132 - 169
13
X-RAY DIFFRACTION
13
C
5 - 35
14
X-RAY DIFFRACTION
14
C
36 - 55
15
X-RAY DIFFRACTION
15
C
56 - 66
16
X-RAY DIFFRACTION
16
C
67 - 95
17
X-RAY DIFFRACTION
17
C
96 - 157
18
X-RAY DIFFRACTION
18
C
158 - 169
19
X-RAY DIFFRACTION
19
D
2 - 30
20
X-RAY DIFFRACTION
20
D
31 - 56
21
X-RAY DIFFRACTION
21
D
57 - 66
22
X-RAY DIFFRACTION
22
D
67 - 96
23
X-RAY DIFFRACTION
23
D
97 - 154
24
X-RAY DIFFRACTION
24
D
155 - 169
25
X-RAY DIFFRACTION
25
E
3 - 29
26
X-RAY DIFFRACTION
26
E
30 - 55
27
X-RAY DIFFRACTION
27
E
56 - 75
28
X-RAY DIFFRACTION
28
E
76 - 96
29
X-RAY DIFFRACTION
29
E
97 - 152
30
X-RAY DIFFRACTION
30
E
153 - 169
31
X-RAY DIFFRACTION
31
F
3 - 28
32
X-RAY DIFFRACTION
32
F
29 - 56
33
X-RAY DIFFRACTION
33
F
57 - 66
34
X-RAY DIFFRACTION
34
F
67 - 96
35
X-RAY DIFFRACTION
35
F
97 - 146
36
X-RAY DIFFRACTION
36
F
147 - 169
+
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