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- PDB-5mmo: E. coli DNA Gyrase B 24 kDa ATPase domain in complex with [3-(3-e... -

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Basic information

Entry
Database: PDB / ID: 5mmo
TitleE. coli DNA Gyrase B 24 kDa ATPase domain in complex with [3-(3-ethyl-ureido)-5-(pyridin-4-yl)-isoquinolin-8-yl-methyl]-carbamic acid prop-2-ynyl ester
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-9JG / PHOSPHATE ION / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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)26,3743
Polymers25,8761
Non-polymers4982
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-7 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.040, 72.040, 79.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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-9JG / prop-2-ynyl ~{N}-[[3-(ethylcarbamoylamino)-5-pyridin-4-yl-isoquinolin-8-yl]methyl]carbamate


Mass: 403.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21N5O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 26-30% (w/v) PEG 4000, 0.1M 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: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.1 Å / Num. obs: 22048 / % possible obs: 99.4 % / Redundancy: 10.8 % / Net I/σ(I): 26.5
Reflection shellLowest resolution: 1.92 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3480

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→49.04 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.148 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.23884 973 5 %RANDOM
Rwork0.18178 ---
obs0.18466 18469 88.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.444 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.81→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 35 125 1732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191664
X-RAY DIFFRACTIONr_bond_other_d0.0020.021564
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9672257
X-RAY DIFFRACTIONr_angle_other_deg0.83133586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71923.91974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68215271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9731511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021904
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02381
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_it2.2742.975837
X-RAY DIFFRACTIONr_mcbond_other2.2732.972836
X-RAY DIFFRACTIONr_mcangle_it3.3264.4381048
X-RAY DIFFRACTIONr_mcangle_other3.3244.4411049
X-RAY DIFFRACTIONr_scbond_it2.9313.299826
X-RAY DIFFRACTIONr_scbond_other2.9113.284823
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5214.7941203
X-RAY DIFFRACTIONr_long_range_B_refined7.01224.8721920
X-RAY DIFFRACTIONr_long_range_B_other6.97624.4551878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.813→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 67 -
Rwork0.27 1259 -
obs--83.24 %

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