DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA unwinding involved in DNA replication / DNA topological change / DNA binding / ATP binding / identical protein binding Similarity search - Function
DNA topoisomerase VI, subunit B / DNA topoisomerase VI, subunit B, transducer / Topoisomerase VI B subunit, transducer / NFACT N-terminal and middle domains / Helicase, Ruva Protein; domain 3 - #50 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Helicase, Ruva Protein; domain 3 ...DNA topoisomerase VI, subunit B / DNA topoisomerase VI, subunit B, transducer / Topoisomerase VI B subunit, transducer / NFACT N-terminal and middle domains / Helicase, Ruva Protein; domain 3 - #50 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Helicase, Ruva Protein; domain 3 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
SEQUENCE Authors state the database/coordinate conflicts for residues 303 and 435 of chains ...SEQUENCE Authors state the database/coordinate conflicts for residues 303 and 435 of chains A,B,C,D,E and F are due to strain-specific sequence differences between the protein in the entry and the database sequence.
#95 - Nov 2007 Multidrug Resistance Transporters similarity (1)
-
Assembly
Deposited unit
A: Type II DNA topoisomerase VI subunit B B: Type II DNA topoisomerase VI subunit B C: Type II DNA topoisomerase VI subunit B D: Type II DNA topoisomerase VI subunit B E: Type II DNA topoisomerase VI subunit B F: Type II DNA topoisomerase VI subunit B hetero molecules
Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.24 / Num. unique all: 13432 / Rsym value: 0.413 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 149698 / % possible obs: 96.1 % / Num. measured all: 2006747 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.8
-
Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
SHARP
phasing
REFMAC
5
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.883 / SU B: 8.174 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Bound nucleotide and MG2+ ions are assigned residue numbers 500 and 501. Residue G1 (NA ION) assigned as NA+ on the basis of coordination. Geometry, short hydrogen bond distances, and low ...Details: Bound nucleotide and MG2+ ions are assigned residue numbers 500 and 501. Residue G1 (NA ION) assigned as NA+ on the basis of coordination. Geometry, short hydrogen bond distances, and low refined b-factor of water when placed in this location.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26327
12535
8.4 %
RANDOM
Rwork
0.21447
-
-
-
all
0.21854
150115
-
-
obs
0.21854
137434
98.1 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 25.95 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.31 Å2
0 Å2
0 Å2
2-
-
0.55 Å2
0 Å2
3-
-
-
-0.86 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
22053
0
193
811
23057
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
22729
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.424
1.982
30805
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.249
3
2741
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.603
15
4417
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
3429
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
16914
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.272
0.3
11373
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.169
1962
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.291
0.3
113
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.272
0.5
17
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_mcbond_it
0.735
1.5
13787
X-RAY DIFFRACTION
r_mcangle_it
1.397
2
22497
X-RAY DIFFRACTION
r_scbond_it
2.317
3
8942
X-RAY DIFFRACTION
r_scangle_it
3.849
4.5
8308
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.3→2.359 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.307
791
Rwork
0.257
8944
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
0.1283
-0.0593
0.0234
0.7211
0.1089
0.3938
-0.0303
-0.0138
-0.0194
-0.0166
0.0707
0.0005
-0.0958
-0.013
-0.0404
0.3555
0.0046
0.0258
0.3074
0.0074
0.3269
48.9394
38.3139
23.4422
2
2.8612
-0.2428
0.4455
2.2588
1.4704
3.798
0.1446
0.1101
-0.0633
0.2435
0.1955
-0.2157
0.2704
0.347
-0.34
0.2757
0.068
-0.0832
0.2997
-0.0781
0.312
73.0341
16.9634
44.227
3
1.4857
-0.4459
-0.3706
1.484
0.4504
1.7467
0.0025
-0.1996
-0.1694
0.1927
0.0715
0.1613
-0.0218
-0.2014
-0.074
0.3244
0.032
0.0518
0.3608
0.0689
0.3029
40.357
29.0794
49.8905
4
0.4391
0.0842
0.0459
1.0768
-0.0474
0.2619
0.0201
0.0094
-0.0557
0.0582
0.0962
-0.0703
0.0326
-0.0056
-0.1163
0.3056
0.0116
-0.0288
0.2812
0.0031
0.3623
52.6117
1.5366
25.1796
5
2.7359
2.0486
-0.4248
4.3386
-1.1169
2.4712
-0.1613
0.0657
-0.0424
-0.3977
0.1544
-0.0323
0.0172
-0.0004
0.007
0.313
-0.0171
0.0139
0.2759
0.0124
0.2693
38.492
23.4858
-2.6595
6
1.6321
0.1178
-0.2663
1.2672
-0.4598
0.9132
-0.0004
-0.0909
-0.103
0.0945
0.094
0.1508
-0.0693
-0.0926
-0.0937
0.2751
0.0082
0.0024
0.3079
0.0666
0.365
25.3967
9.121
25.6661
7
0.2531
0.0985
-0.3874
0.3492
-0.081
0.7633
-0.0555
-0.0549
-0.0059
0.0684
0.0558
0.0263
0.0429
0.1354
-0.0002
0.3145
0.0512
-0.0066
0.4061
0.0117
0.293
148.6915
46.147
43.0581
8
2.2705
0.0954
-1.0722
1.4593
-1.0951
2.8878
-0.0462
0.0015
-0.0684
-0.0607
-0.0853
-0.0139
0.1777
0.1144
0.1315
0.2905
0.0645
-0.0007
0.3109
-0.0021
0.2898
157.4891
27.0817
11.375
9
2.0351
0.6939
-0.4379
0.6963
0.1404
0.1778
0.0181
-0.0269
-0.0116
0.0744
-0.0669
0.1112
0.0222
0.0206
0.0488
0.3159
0.0107
0.0214
0.3278
0.0161
0.3378
126.5376
32.7397
27.8624
10
0.4071
-0.1462
0.0458
0.4277
-0.0786
0.6354
0.0062
-0.0064
-0.0183
-0.067
-0.0177
0.0077
-0.0274
0.0795
0.0115
0.3272
0.0242
-0.0243
0.3375
-0.0014
0.3061
149.0087
57.4523
7.6374
11
2.3417
-0.3646
1.1609
1.5167
0.1313
2.0852
-0.0266
-0.1517
0.0529
0.0028
0.0351
-0.0067
-0.1926
0.1415
-0.0085
0.3263
-0.0236
-0.0102
0.3314
-0.0611
0.2601
151.5591
77.6155
40.0348
12
1.7609
-0.4387
0.4255
0.85
-0.0703
1.6094
0.0119
-0.0542
-0.0638
0.0189
0.0495
0.0809
-0.0407
-0.1724
-0.0614
0.3101
0.0256
-0.0133
0.3446
0.0086
0.2886
124.8533
66.1872
21.1324
13
0.8641
-0.0256
0.2777
0.4351
0.1866
0.5058
0.062
0.1355
-0.0653
0.0189
0.0196
-0.005
0.011
0.0702
-0.0816
0.3322
0.0262
-0.0154
0.3279
-0.0137
0.3211
119.6947
35.7404
-32.0975
14
4.4131
-2.9668
0.4878
5.7435
0.3339
2.6045
0.2985
-0.1628
-0.3702
0.0705
0.0808
-0.2219
0.136
0.0875
-0.3793
0.2409
0.0386
-0.2283
0.1552
0.0146
0.4373
139.2867
13.8784
-7.5551
15
2.0442
-0.838
0.1236
1.8916
0.7674
0.9116
0.0052
-0.345
-0.1717
0.1624
0.0778
0.0735
0.0579
-0.0772
-0.083
0.3073
-0.0086
-0.0155
0.3644
0.0787
0.2863
110.775
33.1981
-4.9806
16
1.8314
0.9246
0.7705
0.7601
0.0951
1.1414
0.7314
0.0733
-0.7981
0.212
0.0082
-0.4615
0.5861
0.119
-0.7396
0.5795
0.02
-0.5386
0.0056
0.0105
0.7162
115.0182
0.5892
-22.9146
17
6.523
2.5525
-0.0349
1.5178
0.2438
2.0034
0.0811
1.118
-0.6969
0.0547
0.2312
-0.2114
-0.096
0.1077
-0.3124
0.25
0.0923
-0.0575
0.4763
-0.2373
0.2851
104.4745
19.4135
-54.5413
18
4.4682
0.6011
-0.7242
1.1986
-0.4575
2.9782
0.4724
-0.3212
-0.455
0.2709
-0.0096
-0.0184
0.2273
-0.3636
-0.4628
0.3838
-0.1396
-0.1724
0.2382
0.1628
0.3469
89.6417
12.9344
-24.1531
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
4 - 229
6 - 231
2
X-RAY DIFFRACTION
2
A
A
230 - 310
232 - 312
3
X-RAY DIFFRACTION
3
A
A
311 - 467
313 - 469
4
X-RAY DIFFRACTION
4
B
B
4 - 229
6 - 231
5
X-RAY DIFFRACTION
5
B
B
230 - 310
232 - 312
6
X-RAY DIFFRACTION
6
B
B
311 - 458
313 - 460
7
X-RAY DIFFRACTION
7
C
C
4 - 229
6 - 231
8
X-RAY DIFFRACTION
8
C
C
230 - 310
232 - 312
9
X-RAY DIFFRACTION
9
C
C
311 - 469
313 - 471
10
X-RAY DIFFRACTION
10
D
D
4 - 229
6 - 231
11
X-RAY DIFFRACTION
11
D
D
230 - 310
232 - 312
12
X-RAY DIFFRACTION
12
D
D
311 - 464
313 - 466
13
X-RAY DIFFRACTION
13
E
E
4 - 229
6 - 231
14
X-RAY DIFFRACTION
14
E
E
230 - 310
232 - 312
15
X-RAY DIFFRACTION
15
E
E
311 - 461
313 - 463
16
X-RAY DIFFRACTION
16
F
F
4 - 229
6 - 231
17
X-RAY DIFFRACTION
17
F
F
230 - 310
232 - 312
18
X-RAY DIFFRACTION
18
F
F
311 - 463
313 - 465
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
r_bond_d
0.013
X-RAY DIFFRACTION
r_angle_d
X-RAY DIFFRACTION
r_angle_deg
1.423
+
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