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- PDB-7dpr: E. coli GyrB ATPase domain in complex with methyl 3,4-dihydroxybe... -

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Basic information

Entry
Database: PDB / ID: 7dpr
TitleE. coli GyrB ATPase domain in complex with methyl 3,4-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 3,4-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: 1.75 Å
AuthorsYu, Y. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
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 21, 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)46,24110
Polymers45,2972
Non-polymers9448
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-17 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.973, 67.389, 102.365
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-HE9 / methyl 3,4-bis(oxidanyl)benzoate


Mass: 168.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AX7 / 1H-benzimidazol-2-amine


Mass: 133.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
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: 1.75→56.29 Å / Num. obs: 43063 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Χ2: 2.654 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.786.40.46921420.9030.20.5110.507100
1.78-1.815.90.39520900.9180.1760.4330.5599.7
1.81-1.856.60.36421360.9360.1520.3950.594100
1.85-1.896.80.35621110.9510.1450.3850.813100
1.89-1.936.80.3421390.9640.1390.3680.95299.9
1.93-1.976.70.21421210.970.0890.2320.904100
1.97-2.026.70.17421240.9660.0730.1890.84399.9
2.02-2.076.50.24621190.3270.110.271.536100
2.07-2.146.40.13521310.9770.0570.1471.25499.9
2.14-2.260.11821300.960.0520.1291.85799.4
2.2-2.286.80.15221350.9770.0620.1651.599100
2.28-2.386.80.09121270.9830.0380.0991.67299.9
2.38-2.486.70.08121650.9870.0340.0881.55100
2.48-2.616.70.07721370.9830.0320.0842.09999.9
2.61-2.786.30.08321630.9750.0350.0913.32599.6
2.78-2.996.60.06121490.9870.0250.0663.1299.9
2.99-3.296.80.05421790.9820.0230.0593.736100
3.29-3.776.60.05822080.9780.0240.0625.953100
3.77-4.756.20.04822120.9850.020.0528.75399.6
4.75-506.20.05723450.9750.0250.06310.971100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z9B

5z9b


Resolution: 1.75→56.29 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25235 2179 5.1 %RANDOM
Rwork0.22463 ---
obs0.22605 40825 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.229 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å20 Å2
2--1.55 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.75→56.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 59 186 3132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192992
X-RAY DIFFRACTIONr_bond_other_d00.022759
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9524050
X-RAY DIFFRACTIONr_angle_other_deg3.6836374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0015369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54524.058138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65615503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5511521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023466
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02595
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_it0.5742.7431488
X-RAY DIFFRACTIONr_mcbond_other0.5742.7421487
X-RAY DIFFRACTIONr_mcangle_it1.0444.1081853
X-RAY DIFFRACTIONr_mcangle_other1.0444.1091854
X-RAY DIFFRACTIONr_scbond_it0.5352.8121504
X-RAY DIFFRACTIONr_scbond_other0.5372.7991485
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.894.1682168
X-RAY DIFFRACTIONr_long_range_B_refined2.31932.4223245
X-RAY DIFFRACTIONr_long_range_B_other2.26632.2253213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.752→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 165 -
Rwork0.267 2917 -
obs--98.18 %

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