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- PDB-5z9l: Bacterial GyrB ATPase domain in complex with a chemical fragment -

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Basic information

Entry
Database: PDB / ID: 5z9l
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) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) 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) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) 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
2-fluoro-4-hydroxybenzonitrile / 1H-benzimidazol-2-amine / PHOSPHATE ION / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)46,1989
Polymers45,4112
Non-polymers7877
Water2,882160
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0334
Polymers22,7051
Non-polymers3273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-3 kcal/mol
Surface area9130 Å2
MethodPISA
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1665
Polymers22,7051
Non-polymers4604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-4 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.070, 69.065, 102.121
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-8H8 / 2-fluoro-4-hydroxybenzonitrile


Mass: 137.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4FNO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AX7 / 1H-benzimidazol-2-amine


Mass: 133.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl pH 7.5, 2.20M (NH4)2HPO4, 10mM 2-aminobenzimidazole

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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: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→57.22 Å / Num. obs: 55927 / % possible obs: 96.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.8
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7422 / % possible all: 89.6

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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: 1.6→57.21 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.004 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24166 2762 5 %RANDOM
Rwork0.22822 ---
obs0.22889 53016 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.039 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20 Å2
2--0.62 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.6→57.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 50 160 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192975
X-RAY DIFFRACTIONr_bond_other_d0.0060.022812
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9474032
X-RAY DIFFRACTIONr_angle_other_deg0.9436441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99523.731134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65515493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3351522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02678
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_it0.9691.9621493
X-RAY DIFFRACTIONr_mcbond_other0.9661.9611492
X-RAY DIFFRACTIONr_mcangle_it1.6572.9331861
X-RAY DIFFRACTIONr_mcangle_other1.6572.9331862
X-RAY DIFFRACTIONr_scbond_it1.2022.1581482
X-RAY DIFFRACTIONr_scbond_other1.2022.1581483
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9873.1672171
X-RAY DIFFRACTIONr_long_range_B_refined3.74915.8523211
X-RAY DIFFRACTIONr_long_range_B_other3.74815.8533212
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 174 -
Rwork0.238 3370 -
obs--84.16 %
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)
10.21280.19260.05350.31330.26770.3606-0.01730.00630.03550.00870.01040.03040.02780.01350.0070.0323-0.0161-0.00940.01110.00480.00743.1692-16.768816.4667
20.32770.09960.29460.0630.05560.3002-0.0124-0.00820.0491-0.0226-0.0180.02780.01130.00620.03050.0254-0.00430.0020.0184-0.01730.021728.957710.55269.3965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 219
2X-RAY DIFFRACTION2B16 - 220

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