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- PDB-6m1s: The DNA Gyrase B ATP binding domain of PSEUDOMONAS AERUGINOSA in ... -

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Basic information

Entry
Database: PDB / ID: 6m1s
TitleThe DNA Gyrase B ATP binding domain of PSEUDOMONAS AERUGINOSA in complex with compound 12o
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-EZ9 / DNA gyrase subunit B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.254 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)49,1978
Polymers47,8802
Non-polymers1,3176
Water1,44180
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5933
Polymers23,9401
Non-polymers6542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area9430 Å2
MethodPISA
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6045
Polymers23,9401
Non-polymers6644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.694, 46.928, 89.862
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0

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Components

#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)
#2: Chemical ChemComp-EZ9 / 3-[5-[8-(ethylamino)-6-fluoranyl-4-[3-(trifluoromethyl)pyrazol-1-yl]-9H-pyrido[2,3-b]indol-3-yl]pyrimidin-2-yl]oxy-2,2-dimethyl-propanoic acid


Mass: 557.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H23F4N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 38.00%w/v PEG3350, 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: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.254→31.074 Å / Num. obs: 21976 / % possible obs: 98.95 % / Redundancy: 4.6 % / Biso Wilson estimate: 32.43 Å2 / Rpim(I) all: 0.061 / Net I/σ(I): 13.45
Reflection shellResolution: 2.254→2.29 Å / Num. unique obs: 1054 / CC1/2: 0.728

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KFG

4kfg


Resolution: 2.254→31.074 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.65
RfactorNum. reflection% reflection
Rfree0.2617 1053 4.79 %
Rwork0.2031 --
obs0.2061 21976 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.37 Å2 / Biso mean: 43.537 Å2 / Biso min: 16.73 Å2
Refinement stepCycle: final / Resolution: 2.254→31.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 88 80 3181
Biso mean--35.7 43.04 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093177
X-RAY DIFFRACTIONf_angle_d1.1874313
X-RAY DIFFRACTIONf_chiral_restr0.052466
X-RAY DIFFRACTIONf_plane_restr0.005551
X-RAY DIFFRACTIONf_dihedral_angle_d16.0471137
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1659X-RAY DIFFRACTION11.595TORSIONAL
12B1659X-RAY DIFFRACTION11.595TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.254-2.35650.34471100.2646255898
2.3565-2.48070.34011200.2681256899
2.4807-2.63610.29951360.2678258499
2.6361-2.83950.31511270.2488257799
2.8395-3.1250.27711330.2286261499
3.125-3.57660.25741330.1837261199
3.5766-4.50390.22411300.16552671100
4.5039-31.0740.2341640.178274098
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)
11.5789-0.4064-0.35594.9722-0.51592.45890.0170.0323-0.16860.11550.08260.62260.0473-0.2535-0.05360.1734-0.0253-0.01770.276-0.00980.275116.626812.139938.0627
21.4605-0.33980.55042.029-0.02852.10120.0465-0.0608-0.05210.2428-0.0834-0.09720.07990.07610.02810.3557-0.0655-0.0130.2538-0.00480.199127.843321.544111.451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A17 - 221
2X-RAY DIFFRACTION2chain 'B'B17 - 222

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