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- PDB-7dqu: E. coli GyrB ATPase domain in complex with methyl 4-hydroxybenzoate -

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Basic information

Entry
Database: PDB / ID: 7dqu
TitleE. coli GyrB ATPase domain in complex with methyl 4-hydroxybenzoate
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 / 4-HYDROXY-BENZOIC ACID METHYL ESTER / PHOSPHATE ION / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 24, 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)46,0198
Polymers45,2972
Non-polymers7226
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-8 kcal/mol
Surface area17380 Å2
Unit cell
Length a, b, c (Å)61.165, 68.514, 102.454
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)
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-MPB / 4-HYDROXY-BENZOIC ACID METHYL ESTER


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / 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.: 81 / 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: 48.09 %
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: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.88→56.95 Å / Num. obs: 35434 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.984 / Net I/σ(I): 20.04
Reflection shellResolution: 1.88→1.95 Å / Num. unique obs: 3492 / CC1/2: 0.854

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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: 1.88→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.75 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25522 1754 5 %RANDOM
Rwork0.23667 ---
obs0.23755 33629 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.669 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0 Å2
2--1.29 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 47 81 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192948
X-RAY DIFFRACTIONr_bond_other_d0.0010.022716
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.9473994
X-RAY DIFFRACTIONr_angle_other_deg0.85336259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9045369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62523.91133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.19715482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1891521
X-RAY DIFFRACTIONr_chiral_restr0.0590.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
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_it0.6332.7311488
X-RAY DIFFRACTIONr_mcbond_other0.6332.731487
X-RAY DIFFRACTIONr_mcangle_it1.1574.091853
X-RAY DIFFRACTIONr_mcangle_other1.1574.0911854
X-RAY DIFFRACTIONr_scbond_it0.5152.791460
X-RAY DIFFRACTIONr_scbond_other0.5152.7761449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.94.1342124
X-RAY DIFFRACTIONr_long_range_B_refined1.94731.4883013
X-RAY DIFFRACTIONr_long_range_B_other1.91231.4352997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.881→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 148 -
Rwork0.296 2433 -
obs--98.36 %

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