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- PDB-5z9m: Bacterial GyrB ATPase domain in complex with a chemical fragment -

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Basic information

Entry
Database: PDB / ID: 5z9m
TitleBacterial GyrB ATPase domain in complex with a chemical fragment
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / DNA Topoisomerase / Antibacterial / Drug Target / Fragment-base Lead Discovery
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / cytosol / 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
1-benzofuran-2-carboxylic acid / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsHuang, X. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81773636 China
CitationJournal: Medchemcomm / Year: 2018
Title: Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes
Authors: Huang, X. / Guo, J. / Liu, Q. / Gu, Q. / Xu, J. / Zhou, H.
History
DepositionFeb 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,79215
Polymers45,4112
Non-polymers1,38113
Water90150
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,63610
Polymers22,7051
Non-polymers9319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1565
Polymers22,7051
Non-polymers4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.380, 101.790, 104.860
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 / Type IIA topoisomerase subunit GyrB


Mass: 22705.473 Da / Num. of mol.: 2 / Fragment: UNP residues 15-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12
Gene: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625
Production host: Escherichia coli (E. coli) / References: UniProt: P0AES6, EC: 5.99.1.3
#2: Chemical ChemComp-BZ2 / 1-benzofuran-2-carboxylic acid


Mass: 162.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 5.72 Å3/Da / Density % sol: 78.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH 6.0, 2.5M MgSO4, 8mM Tris-(2-carboxyethyl)phosphine (TECP).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.74→73.04 Å / Num. obs: 27942 / % possible obs: 93.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.4
Reflection shellResolution: 2.74→2.88 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 3447 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DUH

4duh


Resolution: 2.74→73.04 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.338 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21697 1368 5.3 %RANDOM
Rwork0.1996 ---
obs0.20048 24332 91.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.309 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å2-0 Å20 Å2
2--3.77 Å20 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 2.74→73.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 79 50 2957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192949
X-RAY DIFFRACTIONr_bond_other_d00.022688
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9494014
X-RAY DIFFRACTIONr_angle_other_deg3.81136139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5325371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53723.91133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94415446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.3671520
X-RAY DIFFRACTIONr_chiral_restr0.0670.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023469
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02669
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_it2.2645.421496
X-RAY DIFFRACTIONr_mcbond_other2.2625.421495
X-RAY DIFFRACTIONr_mcangle_it3.7958.121863
X-RAY DIFFRACTIONr_mcangle_other3.7948.1211864
X-RAY DIFFRACTIONr_scbond_it3.1365.891453
X-RAY DIFFRACTIONr_scbond_other2.8185.7461408
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7928.4922084
X-RAY DIFFRACTIONr_long_range_B_refined7.4142.162989
X-RAY DIFFRACTIONr_long_range_B_other7.25441.9452974
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.743→2.814 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 111 -
Rwork0.289 1781 -
obs--93.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3784-0.1842-0.04070.17670.07080.1534-0.00780.0404-0.02270.0046-0.00330.017-0.0176-0.00530.01110.01020.00430.01520.0213-0.00020.0389-39.16988.9976-7.2797
20.28540.1226-0.05610.204-0.13720.38020.02780.0283-0.01480.04260.0085-0.04450.0053-0.0069-0.03620.02060.0037-0.00380.00350.00380.0495-17.421115.378515.5638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 219
2X-RAY DIFFRACTION2B16 - 219

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