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- PDB-7dqh: E. coli GyrB ATPase domain in complex with 2-hydroxybenzamide -

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Basic information

Entry
Database: PDB / ID: 7dqh
TitleE. coli GyrB ATPase domain in complex with 2-hydroxybenzamide
ComponentsDNA gyrase subunit B
KeywordsISOMERASE
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
DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, 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 gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, 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 / 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
1H-benzimidazol-2-amine / salicylamide / PHOSPHATE ION / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsYu, Y. / Zhou, H.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Bioorg.Chem. / Year: 2021
Title: Identification of new building blocks by fragment screening for discovering GyrB inhibitors.
Authors: Yu, Y. / Guo, J. / Cai, Z. / Ju, Y. / Xu, J. / Gu, Q. / Zhou, H.
History
DepositionDec 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)45,9898
Polymers45,2972
Non-polymers6926
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-10 kcal/mol
Surface area17480 Å2
Unit cell
Length a, b, c (Å)61.517, 67.646, 102.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA gyrase subunit B


Mass: 22648.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: gyrB, FAZ83_13380 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A4S5B230, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-AX7 / 1H-benzimidazol-2-amine


Mass: 133.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N3
#3: Chemical ChemComp-OHB / salicylamide / 2-hydroxybenzamide


Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 7.5, 2.20 M (NH4)2HPO4, 10 mM 2-aminobenzimidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97907 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.91→56.42 Å / Num. obs: 33972 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.965 / Net I/σ(I): 30.349
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 1660 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z9B

5z9b


Resolution: 1.91→56.42 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23445 1658 4.9 %RANDOM
Rwork0.20079 ---
obs0.2025 32261 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--3.03 Å2-0 Å2
3----3.06 Å2
Refinement stepCycle: 1 / Resolution: 1.91→56.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 45 162 3082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192968
X-RAY DIFFRACTIONr_bond_other_d00.022732
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.9474019
X-RAY DIFFRACTIONr_angle_other_deg3.81136309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38724.058138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11515495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9631521
X-RAY DIFFRACTIONr_chiral_restr0.140.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02596
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_it4.1723.511484
X-RAY DIFFRACTIONr_mcbond_other4.173.511483
X-RAY DIFFRACTIONr_mcangle_it5.0945.231848
X-RAY DIFFRACTIONr_mcangle_other5.0945.2311849
X-RAY DIFFRACTIONr_scbond_it5.3323.9791484
X-RAY DIFFRACTIONr_scbond_other5.3113.9661471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1055.7532153
X-RAY DIFFRACTIONr_long_range_B_refined8.59642.4753220
X-RAY DIFFRACTIONr_long_range_B_other8.60642.3383196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.955 Å
RfactorNum. reflection% reflection
Rfree0.27 105 -
Rwork0.304 2266 -
obs--96.3 %

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