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- PDB-5mmp: E. coli DNA Gyrase B 24 kDa ATPase domain in complex with 1-ethyl... -

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Basic information

Entry
Database: PDB / ID: 5mmp
TitleE. coli DNA Gyrase B 24 kDa ATPase domain in complex with 1-ethyl-3-[5-pyridin-4-yl-8-(pyridin-3-ylamino)-isoquinolin-3-yl]-urea
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / Inhibitor / 009
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
: / 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-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-G3Z / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPanchaud, P. / Bruyere, T. / Blumstein, A.-C. / Bur, D. / Chambovey, A. / Ertel, E.A. / Gude, M. / Hubschwerlen, C. / Jacob, L. / Kimmerlin, T. ...Panchaud, P. / Bruyere, T. / Blumstein, A.-C. / Bur, D. / Chambovey, A. / Ertel, E.A. / Gude, M. / Hubschwerlen, C. / Jacob, L. / Kimmerlin, T. / Pfeifer, T. / Prade, L. / Seiler, P. / Ritz, D. / Rueedi, G.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery and Optimization of Isoquinoline Ethyl Ureas as Antibacterial Agents.
Authors: Panchaud, P. / Bruyere, T. / Blumstein, A.C. / Bur, D. / Chambovey, A. / Ertel, E.A. / Gude, M. / Hubschwerlen, C. / Jacob, L. / Kimmerlin, T. / Pfeifer, T. / Prade, L. / Seiler, P. / Ritz, D. / Rueedi, G.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2602
Polymers25,8761
Non-polymers3841
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.640, 102.640, 48.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA gyrase subunit B /


Mass: 25876.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: gyrB, Z5190, ECs4634 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AES7, EC: 5.99.1.3
#2: Chemical ChemComp-G3Z / 1-ethyl-3-[5-pyridin-4-yl-8-(pyridin-3-ylamino)isoquinolin-3-yl]urea


Mass: 384.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 26-30% (w/v) PEG 4000, 0.1 M sodium/potassium phosphate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→42.6 Å / Num. obs: 35162 / % possible obs: 98.1 % / Redundancy: 21.6 % / Net I/σ(I): 21.6
Reflection shellResolution: 2.05→2.18 Å / Mean I/σ(I) obs: 4.48 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→35.28 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.883 / SU B: 3.152 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.25783 862 5 %RANDOM
Rwork0.22074 ---
obs0.2226 16364 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 27.266 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 2.05→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 29 101 1622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211571
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9712126
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3485193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59124.1173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98915272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4751511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211191
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7951.5954
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50921547
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1933617
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6974.5579
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 57 -
Rwork0.232 1075 -
obs--100 %

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