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- PDB-7dqf: E. coli GyrB ATPase domain in complex with methyl 2,4-dihydroxybe... -

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Basic information

Entry
Database: PDB / ID: 7dqf
TitleE. coli GyrB ATPase domain in complex with methyl 2,4-dihydroxybenzoate
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 / methyl 2,4-bis(oxidanyl)benzoate / PHOSPHATE ION / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)45,9567
Polymers45,2972
Non-polymers6595
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-3 kcal/mol
Surface area17310 Å2
Unit cell
Length a, b, c (Å)61.096, 68.159, 102.397
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-HF9 / methyl 2,4-bis(oxidanyl)benzoate


Mass: 168.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.8→56.74 Å / Num. obs: 40376 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.976 / Net I/σ(I): 22.88
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1984 / CC1/2: 0.891

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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: 1.8→56.74 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24933 2031 5 %RANDOM
Rwork0.21808 ---
obs0.21967 38290 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: 26.029 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0 Å2-0 Å2
2--1.38 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: 1 / Resolution: 1.8→56.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 44 106 3024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192966
X-RAY DIFFRACTIONr_bond_other_d00.022750
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9484014
X-RAY DIFFRACTIONr_angle_other_deg3.70736348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.845369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.59524135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41815498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8221521
X-RAY DIFFRACTIONr_chiral_restr0.110.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023436
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02593
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_it1.5692.4881488
X-RAY DIFFRACTIONr_mcbond_other1.5662.4871487
X-RAY DIFFRACTIONr_mcangle_it2.3843.7121853
X-RAY DIFFRACTIONr_mcangle_other2.3843.7131854
X-RAY DIFFRACTIONr_scbond_it1.9932.8281478
X-RAY DIFFRACTIONr_scbond_other1.9852.7411471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.124.0072150
X-RAY DIFFRACTIONr_long_range_B_refined6.71930.0013216
X-RAY DIFFRACTIONr_long_range_B_other6.73629.9143199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.844 Å
RfactorNum. reflection% reflection
Rfree0.301 126 -
Rwork0.27 2720 -
obs--97.07 %

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