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- PDB-3g75: Crystal structure of Staphylococcus aureus Gyrase B co-complexed ... -

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Basic information

Entry
Database: PDB / ID: 3g75
TitleCrystal structure of Staphylococcus aureus Gyrase B co-complexed with 4-METHYL-5-[3-(METHYLSULFANYL)-1H-PYRAZOL-5-YL]-2-THIOPHEN-2-YL-1,3-THIAZOLE inhibitor
ComponentsDNA gyrase subunit B
KeywordsIsomerase/Isomerase inhibitor / Antibiotic resistance / Isomerase / Isomerase-Isomerase inhibitor complex
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 / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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. ...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-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-B48 / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWei, Y. / Charifson, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Discovery of pyrazolthiazoles as novel and potent inhibitors of bacterial gyrase.
Authors: Ronkin, S.M. / Badia, M. / Bellon, S. / Grillot, A.L. / Gross, C.H. / Grossman, T.H. / Mani, N. / Parsons, J.D. / Stamos, D. / Trudeau, M. / Wei, Y. / Charifson, P.S.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)42,8424
Polymers42,2552
Non-polymers5872
Water5,873326
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4212
Polymers21,1281
Non-polymers2931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4212
Polymers21,1281
Non-polymers2931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.470, 57.600, 50.940
Angle α, β, γ (deg.)90.00, 97.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA gyrase subunit B


Mass: 21127.588 Da / Num. of mol.: 2 / Fragment: residues 24-230 / Mutation: Deletion residues 105-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0K8, EC: 5.99.1.3
#2: Chemical ChemComp-B48 / 4-methyl-5-[3-(methylsulfanyl)-1H-pyrazol-5-yl]-2-thiophen-2-yl-1,3-thiazole


Mass: 293.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11N3S3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: hanging drop, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2008 / Details: mirrors
RadiationMonochromator: Ni mirrors + Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 18736 / Num. obs: 15364 / % possible obs: 82 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.3→2.5 Å / % possible all: 60

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNX2005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.92 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 4364711.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.34 755 5 %RANDOM
Rwork0.244 ---
obs0.249 15165 81.1 %-
all-15340 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 133.599 Å2 / ksol: 0.61198 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-14.37 Å2
2---9.67 Å20 Å2
3---10.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 36 326 3292
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 88 5 %
Rwork0.296 1658 -
obs--56.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.pprotein.top
X-RAY DIFFRACTION2016261.par016261.top
X-RAY DIFFRACTION3water_rep.parwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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