DNA negative supercoiling activity / 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 topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding ...DNA negative supercoiling activity / 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 topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
B: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A D: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A E: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3' F: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3' G: 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3' H: 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3' S: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A U: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A V: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3' W: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3' X: 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3' Y: 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3' hetero molecules
B: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A D: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A E: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3' F: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3' G: 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3' H: 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3' hetero molecules
S: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A U: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A V: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3' W: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3' X: 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3' Y: 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3' hetero molecules
Mass: 331.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18FN3O3 / Comment: antibiotic*YM
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Details
Compound details
ENGINEERED RESIDUE IN CHAIN B, TYR 1123 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 1123 TO PHE ...ENGINEERED RESIDUE IN CHAIN B, TYR 1123 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 1123 TO PHE ENGINEERED RESIDUE IN CHAIN S, TYR 1123 TO PHE ENGINEERED RESIDUE IN CHAIN U, TYR 1123 TO PHE
Sequence details
RESIDUES 544-579 DELETED AND REPLACED WITH TWO AMINO ACIDS, TG. THE C-TERMINUS OF GYRB (6B44) IS ...RESIDUES 544-579 DELETED AND REPLACED WITH TWO AMINO ACIDS, TG. THE C-TERMINUS OF GYRB (6B44) IS FUSED TO THE N- TERMINUS OF GYRA (A2) CATALYTIC TYROSINE (A123/B1123) MUTATED TO PHENYLALANINE. DNA (8MER, 12MER ON TOP 5'-3', 12MER, 8MER UNDER 3'-5') DNA CALLED 8-3NN - FOUR STRANDS (CALLED 8-3,12-3,12-4,8-4) CAN ANNEAL TO GIVE 3 DIFFERENT DUPLEXES 5' TGTGCGGT GTAC- CTACGGCT 8-3 12-3 3' ACACGCCA-CATG GATGCCGA 12-4 8-4 5' TGTGCGGT GTAC-ACCGCACA 8-3 12-3 3' ACACGCCA-CATG TGGCGTGT 12-3 8-3 5' AGCCGTAG GTAC-CTACGGCT 8-4 12-3 3' TCGGCATC- CATG GATGCCGA 12-3 8-4
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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: 2.98 Å3/Da / Density % sol: 58.43 % / Description: NONE
Crystal grow
pH: 6.2 / Details: 11% PEG 3350, 0.15M BIS TRIS PH 6.2
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.933 Å / Relative weight: 1
Reflection twin
Operator: h,-k,-l / Fraction: 0.324
Reflection
Resolution: 3.35→25 Å / Num. obs: 52713 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 76.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.1
Reflection shell
Resolution: 3.35→3.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 98.4
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
MOSFLM
datareduction
SCALA
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→24.956 Å / SU ML: 0 / σ(F): 1.38 / Phase error: 37.56 / Stereochemistry target values: TWIN_LSQ_F Details: THE DATA ARE IN P21, BUT WITH A BETA ANGLE OF 90 DEGREES.BECAUSE THE DATA ARE PSEUDO ORTHORHOMBIC. AUTHOR SELECTED THE R-FREE IN THE ABOVE MENTIONED RESOLUTION SHELLS. THIS IS NOT A STANDARD ...Details: THE DATA ARE IN P21, BUT WITH A BETA ANGLE OF 90 DEGREES.BECAUSE THE DATA ARE PSEUDO ORTHORHOMBIC. AUTHOR SELECTED THE R-FREE IN THE ABOVE MENTIONED RESOLUTION SHELLS. THIS IS NOT A STANDARD SPACE GROUP FOR A TWIN OPERATOR.
Rfactor
Num. reflection
% reflection
Rfree
0.2363
2148
4.1 %
Rwork
0.1664
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-
obs
0.1692
52173
98.47 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.369 Å2 / ksol: 0.291 e/Å3
Displacement parameters
Biso mean: 73.7 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.157 Å2
0 Å2
5.3898 Å2
2-
-
15.7485 Å2
-0 Å2
3-
-
-
-24.7844 Å2
Refinement step
Cycle: LAST / Resolution: 3.35→24.956 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
20781
1461
104
0
22346
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.024
22861
X-RAY DIFFRACTION
f_angle_d
1.442
31150
X-RAY DIFFRACTION
f_dihedral_angle_d
20.472
8689
X-RAY DIFFRACTION
f_chiral_restr
0.082
3550
X-RAY DIFFRACTION
f_plane_restr
0.005
3859
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.35-3.4077
0.3288
141
0.2114
2487
X-RAY DIFFRACTION
98
3.4077-3.4695
0.2875
55
0.2005
2518
X-RAY DIFFRACTION
98
3.4695-3.536
0.2556
86
0.1984
2504
X-RAY DIFFRACTION
98
3.536-3.608
0.2874
141
0.1959
2444
X-RAY DIFFRACTION
98
3.608-3.6862
0.257
141
0.1828
2475
X-RAY DIFFRACTION
98
3.6862-3.7717
0
0
0.1812
2558
X-RAY DIFFRACTION
98
3.7717-3.8657
0.2032
141
0.1759
2494
X-RAY DIFFRACTION
98
3.8657-3.9698
0.2449
141
0.1677
2417
X-RAY DIFFRACTION
98
3.9698-4.0861
0.2281
141
0.1652
2475
X-RAY DIFFRACTION
98
4.0861-4.2174
0
0
0.1544
2597
X-RAY DIFFRACTION
98
4.2174-4.3674
0.2214
141
0.1497
2445
X-RAY DIFFRACTION
98
4.3674-4.5412
0.2045
141
0.1424
2448
X-RAY DIFFRACTION
98
4.5412-4.7465
0.2274
141
0.1439
2501
X-RAY DIFFRACTION
98
4.7465-4.9949
0
0
0.144
2581
X-RAY DIFFRACTION
98
4.9949-5.3051
0.2214
141
0.1477
2483
X-RAY DIFFRACTION
98
5.3051-5.7101
0.2887
141
0.1626
2464
X-RAY DIFFRACTION
98
5.7101-6.2765
0.2968
141
0.1682
2475
X-RAY DIFFRACTION
98
6.2765-7.1658
0
0
0.1809
2637
X-RAY DIFFRACTION
98
7.1658-8.9582
0.2383
141
0.1552
2516
X-RAY DIFFRACTION
98
8.9582-24.9566
0.1763
141
0.1767
2539
X-RAY DIFFRACTION
98
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
0.9306
-0.1717
-0.0791
0.1593
-0.1299
-0.1528
0.0484
0.1751
-0.0667
-0.0529
-0.0047
-0.0022
0.0301
-0.0153
-0.0349
0.3065
0.0282
-0.0383
0.3247
-0.0268
0.3598
13.8303
30.4628
81.7539
2
0.4404
0.101
0.3511
0.24
-0.2218
0.6484
0.0208
0.1688
0.1346
-0.0052
0.0215
0.1235
-0.011
-0.0769
-0.043
0.1651
0.0067
-0.0415
0.1761
0.1026
0.3215
4.8182
62.4552
64.0615
3
0.1366
0.2695
0.162
0.3624
0.1048
0.2254
0.1599
0.0612
-0.0447
-0.1003
-0.185
0.1474
0.0495
0.0155
0.0438
0.31
0.0751
-0.0651
0.2625
-0.0484
0.175
1.0299
42.1024
132.9771
4
0.1111
-0.0409
0.2257
0.4482
-0.1094
0.2157
-0.0103
0.2428
-0.3556
-0.0195
0.0306
0.232
0.003
0.2067
-0.069
0.2531
-0.0284
-0.0291
0.4383
0.1131
0.5869
23.5957
59.8005
72.2793
5
0.2712
-0.1024
0.2324
0.782
-0.4833
0.8966
-0.1512
-0.1006
0.0915
0.0456
0.0608
0.0005
-0.054
-0.1943
0.0605
0.2475
-0.0119
-0.096
0.4002
-0.009
0.3754
-29.7788
51.9111
82.2621
6
0.4959
-0.1105
-0.2882
0.4866
-0.077
-0.2508
0.2332
0.2913
-0.2184
-0.1534
-0.0536
-0.0765
0.1083
0.208
-0.1169
0.3629
0.1225
-0.1026
0.2472
-0.0976
0.2559
-14.0594
17.034
63.1686
7
0.2545
0.0336
-0.1366
0.085
-0.0124
0.0655
-0.0895
-0.0543
-0.0858
0.1676
-0.0302
0.0239
-0.1399
-0.4961
0.0506
0.3405
0.0611
0.0287
0.4251
0.0316
0.1678
-19.1548
38.238
131.8792
8
-0.1375
0.6644
0.0417
0.862
0.4969
0.937
-0.0032
0.0319
-0.1057
-0.1507
0.2564
-0.2364
0.087
-0.2747
-0.1946
0.2539
-0.1125
-0.1239
0.1691
0.0379
0.203
-33.8843
20.0079
69.0069
9
0.8404
-0.2442
-0.6778
-0.1115
0.0369
0.5083
-0.2579
0.0373
-0.2607
0.0267
0.0804
0.103
0.1207
0.1164
0.1081
0.6006
0.0327
0.1363
0.4066
-0.0087
0.4877
57.2887
30.0654
-5.7269
10
0.4629
0.1534
-0.6633
0.2416
0.0477
0.2925
0.101
0.0785
-0.1081
-0.1572
-0.0007
-0.0715
0.082
0.0171
-0.0594
0.8043
-0.0077
0.0077
0.6111
-0.0773
0.5626
27.9663
16.737
-20.8361
11
0.149
0.0342
0.1622
0.1009
-0.0444
0.3383
0.0311
0.0257
-0.0229
-0.0186
-0.148
0.0658
0.1327
0.3027
0.0691
0.3488
0.0841
-0.0435
0.4227
0.0051
0.1548
50.8904
41.431
46.6307
12
0.3818
0.1821
-0.1222
0.0109
-0.6112
1.1373
0.1293
-0.0136
0.0216
0.2183
-0.0331
-0.1302
-0.5768
0.17
-0.0931
0.7044
-0.13
0.1786
0.4511
0.0132
0.5927
67.0846
58.4173
-15.9857
13
0.2732
-0.0365
-0.2229
0.4769
0.3036
0.9825
0.0503
0.0078
0.1025
-0.0657
-0.0047
-0.0172
-0.2148
-0.1392
-0.0122
0.2124
0.0763
0.0174
0.2026
0.0267
0.1874
13.8319
51.5275
0.0035
14
0.281
-0.3059
-0.136
-0.0428
0.226
0.3301
0.4161
0.2216
0.3796
-0.0831
-0.2045
-0.174
-0.6316
-0.0913
-0.1037
0.5135
0.1171
0.1771
0.2477
0.1036
0.3803
46.9071
62.4124
-22.5056
15
0.7138
-0.3821
-0.267
0.8001
-0.0024
0.1366
-0.3674
0.2092
-0.0352
0.3658
0.2052
0.0702
0.0353
0.1231
0.0732
0.2821
-0.0266
0.0428
0.2434
0.0198
0.1697
30.6748
37.7366
48.1567
16
0.9635
1.3892
1.3992
1.3542
-0.2461
1.2318
0.3087
-0.2344
-0.3162
0.2435
-0.0708
-0.4464
-0.2132
-0.2522
-0.1355
0.4805
0.0364
0.0548
0.4646
0.0061
0.447
7.8046
20.7355
-12.5674
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
((CHAINBAND (RESID1029:1374ORRESID1451:1491)) OR (CHAINE) OR (CHAINF) ORCHAING) OR (CHAINH))
2
X-RAY DIFFRACTION
2
((CHAINBAND (RESID417:545ORRESID580:606)))
3
X-RAY DIFFRACTION
3
((CHAINBAND (RESID1375:1450)))
4
X-RAY DIFFRACTION
4
((CHAINBAND (RESID1019:1028)) OR (CHAINBAND (RESID609:637)))
5
X-RAY DIFFRACTION
5
((CHAINDAND (RESID1030:1374ORRESID1451:1491)))
6
X-RAY DIFFRACTION
6
((CHAINDAND (RESID417:545ORRESID580:606)))
7
X-RAY DIFFRACTION
7
((CHAINDAND (RESID1375:1450)))
8
X-RAY DIFFRACTION
8
((CHAINDAND (RESID1010:1028)) OR (CHAINDAND (RESID607:639)))
9
X-RAY DIFFRACTION
9
((CHAINSAND (RESID1029:1374ORRESID1451:1491)) OR (CHAINV) OR (CHAINW) ORCHAINX) OR (CHAINY))