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- PDB-6m1j: The DNA Gyrase B ATP binding domain of PSEUDOMONAS AERUGINOSA in ... -

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Basic information

Entry
Database: PDB / ID: 6m1j
TitleThe DNA Gyrase B ATP binding domain of PSEUDOMONAS AERUGINOSA in complex with compound 12x
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / DNA GYRASE / TOPOISOMERASE / ATPASE DOMAIN
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-EZ6 / DNA gyrase subunit B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsXu, Z.H. / Zhou, Z.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Pyrido[2,3-b]indole Derivatives with Gram-Negative Activity Targeting Both DNA Gyrase and Topoisomerase IV.
Authors: Hu, Y. / Shi, H. / Zhou, M. / Ren, Q. / Zhu, W. / Zhang, W. / Zhang, Z. / Zhou, C. / Liu, Y. / Ding, X. / Shen, H.C. / Yan, S.F. / Dey, F. / Wu, W. / Zhai, G. / Zhou, Z. / Xu, Z. / Ji, Y. / ...Authors: Hu, Y. / Shi, H. / Zhou, M. / Ren, Q. / Zhu, W. / Zhang, W. / Zhang, Z. / Zhou, C. / Liu, Y. / Ding, X. / Shen, H.C. / Yan, S.F. / Dey, F. / Wu, W. / Zhai, G. / Zhou, Z. / Xu, Z. / Ji, Y. / Lv, H. / Jiang, T. / Wang, W. / Xu, Y. / Vercruysse, M. / Yao, X. / Mao, Y. / Yu, X. / Bradley, K. / Tan, X.
History
DepositionFeb 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit B
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2749
Polymers47,8802
Non-polymers1,3947
Water6,215345
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7446
Polymers23,9401
Non-polymers8055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area9570 Å2
MethodPISA
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5293
Polymers23,9401
Non-polymers5902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.216, 160.743, 41.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

21A-607-

HOH

31B-512-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 17:21 or resseq 23 or resseq...
21(chain B and (resseq 17:21 or resseq 23 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 17:21 or resseq 23 or resseq...A17 - 21
121(chain A and (resseq 17:21 or resseq 23 or resseq...A23
131(chain A and (resseq 17:21 or resseq 23 or resseq...A25 - 39
141(chain A and (resseq 17:21 or resseq 23 or resseq...A4136
151(chain A and (resseq 17:21 or resseq 23 or resseq...A0
161(chain A and (resseq 17:21 or resseq 23 or resseq...A119 - 136
171(chain A and (resseq 17:21 or resseq 23 or resseq...A17 - 221
181(chain A and (resseq 17:21 or resseq 23 or resseq...A144 - 1521
191(chain A and (resseq 17:21 or resseq 23 or resseq...A194 - 192
1101(chain A and (resseq 17:21 or resseq 23 or resseq...A17 - 221
1111(chain A and (resseq 17:21 or resseq 23 or resseq...A17 - 221
1121(chain A and (resseq 17:21 or resseq 23 or resseq...A197 - 221
211(chain B and (resseq 17:21 or resseq 23 or resseq...B17 - 21
221(chain B and (resseq 17:21 or resseq 23 or resseq...B23
231(chain B and (resseq 17:21 or resseq 23 or resseq...B25 - 39
241(chain B and (resseq 17:21 or resseq 23 or resseq...B41 - 83
251(chain B and (resseq 17:21 or resseq 23 or resseq...B119 - 13642
261(chain B and (resseq 17:21 or resseq 23 or resseq...B144 - 152
271(chain B and (resseq 17:21 or resseq 23 or resseq...B155 - 160
281(chain B and (resseq 17:21 or resseq 23 or resseq...B162 - 192
291(chain B and (resseq 17:21 or resseq 23 or resseq...B194 - 195
2101(chain B and (resseq 17:21 or resseq 23 or resseq...B197 - 221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA gyrase subunit B


Mass: 23939.787 Da / Num. of mol.: 2 / Fragment: ATP binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: gyrB, PA0004 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9I7C2, DNA topoisomerase (ATP-hydrolysing)

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Non-polymers , 5 types, 352 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EZ6 / 1-[5-[6-fluoranyl-8-(methylamino)-4-[3-(trifluoromethyl)pyrazol-1-yl]-9H-pyrido[2,3-b]indol-3-yl]pyrimidin-2-yl]cyclopropane-1-carboxylic acid


Mass: 511.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H17F4N7O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 38.00%w/v PEG 3350, 200.00mM LiSO4, 100.00mM Sodium citrate (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→35.9265 Å / Num. obs: 50537 / % possible obs: 93.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 17.41 Å2 / Rpim(I) all: 0.069 / Net I/σ(I): 11.59
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2578 / CC1/2: 0.536

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KFG

4kfg


Resolution: 1.701→35.919 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2306 2461 4.87 %
Rwork0.1922 --
obs0.1939 50518 93.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.28 Å2 / Biso mean: 27.0785 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: final / Resolution: 1.701→35.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 93 345 3379
Biso mean--26.3 36.68 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093141
X-RAY DIFFRACTIONf_angle_d0.9224270
X-RAY DIFFRACTIONf_chiral_restr0.066459
X-RAY DIFFRACTIONf_plane_restr0.006548
X-RAY DIFFRACTIONf_dihedral_angle_d22.1581806
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1501X-RAY DIFFRACTION10.654TORSIONAL
12B1501X-RAY DIFFRACTION10.654TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7013-1.7340.30161290.2843272496
1.734-1.76940.31191530.2746267697
1.7694-1.80790.30811370.2605273297
1.8079-1.84990.31811600.2604266796
1.8499-1.89620.28531610.2324270896
1.8962-1.94740.24891190.215269696
1.9474-2.00470.24181220.1996270795
2.0047-2.06940.22141410.1895270396
2.0694-2.14340.21251380.1846267195
2.1434-2.22920.24291420.1905267095
2.2292-2.33060.231490.1866264194
2.3306-2.45350.21421500.1828265594
2.4535-2.60720.25561370.1864264993
2.6072-2.80840.20591050.1837265592
2.8084-3.09090.22821070.1887265891
3.0909-3.53780.21341440.1741258390
3.5378-4.45590.18311390.1607261090
4.4559-35.9190.22721280.1911265286
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.3724-0.19610.10020.81950.16331.89430.05220.0055-0.0221-0.02880.0155-0.0720.0208-0.0052-0.05080.09630.0050.00010.0575-0.02010.088418.996363.773150.6117
22.6315-0.99140.9321.8565-0.1221.275-0.124-0.3907-0.04150.10590.11120.0051-0.0189-0.0130.02050.15330.0277-0.02860.2331-0.00340.182319.111827.462348.1139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A17 - 221
2X-RAY DIFFRACTION2chain 'B'B17 - 221

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