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- PDB-8bn6: Pseudomonas aeruginosa DNA gyrase B 24kDa ATPase subdomain comple... -

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Basic information

Entry
Database: PDB / ID: 8bn6
TitlePseudomonas aeruginosa DNA gyrase B 24kDa ATPase subdomain complexed with EBL3021
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / DNA GYRASE / GYRB / INHIBITOR / ANTIBACTERIAL / ISOMERASE
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
: / 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-, 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
Chem-R53 / DNA gyrase subunit B
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDurcik, M. / Zega, A. / Zidar, N. / Ilas, J. / Tomasic, T. / Masic, L.P. / Mundy, J.E.A. / Stevenson, C.E.M. / Burton, N. / Lawson, D.M. ...Durcik, M. / Zega, A. / Zidar, N. / Ilas, J. / Tomasic, T. / Masic, L.P. / Mundy, J.E.A. / Stevenson, C.E.M. / Burton, N. / Lawson, D.M. / Maxwell, A. / Kikelj, D.
Funding support Slovenia, European Union, United Kingdom, 7items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0208 Slovenia
Slovenian Research AgencyJ1-9192 Slovenia
Slovenian Research AgencyBI-HU/19-20-008 Slovenia
European Communitys Seventh Framework Programme115583European Union
Wellcome Trust110072/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012523/1 United Kingdom
European Research Council (ERC)H2020-ERC-2014-CoG 648364European Union
CitationJournal: J.Med.Chem. / Year: 2023
Title: New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus .
Authors: Durcik, M. / Cotman, A.E. / Toplak, Z. / Mozina, S. / Skok, Z. / Szili, P.E. / Czikkely, M. / Maharramov, E. / Vu, T.H. / Piras, M.V. / Zidar, N. / Ilas, J. / Zega, A. / Trontelj, J. / ...Authors: Durcik, M. / Cotman, A.E. / Toplak, Z. / Mozina, S. / Skok, Z. / Szili, P.E. / Czikkely, M. / Maharramov, E. / Vu, T.H. / Piras, M.V. / Zidar, N. / Ilas, J. / Zega, A. / Trontelj, J. / Pardo, L.A. / Hughes, D. / Huseby, D. / Berruga-Fernandez, T. / Cao, S. / Simoff, I. / Svensson, R. / Korol, S.V. / Jin, Z. / Vicente, F. / Ramos, M.C. / Mundy, J.E.A. / Maxwell, A. / Stevenson, C.E.M. / Lawson, D.M. / Glinghammar, B. / Sjostrom, E. / Bohlin, M. / Oreskar, J. / Alver, S. / Janssen, G.V. / Sterk, G.J. / Kikelj, D. / Pal, C. / Tomasic, T. / Peterlin Masic, L.
History
DepositionNov 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0May 24, 2023Group: Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 2.1Feb 7, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0734
Polymers24,5371
Non-polymers5353
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-17 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.200, 115.650, 38.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA gyrase subunit B /


Mass: 24537.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: corresponds to residues 1-221 of full-length wild-type protein
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: gyrB, PA0004 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9I7C2, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-R53 / 2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-morpholin-4-yl-1,3-benzothiazole-6-carboxylic acid


Mass: 455.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16Cl2N4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.06 Å3/Da / Density % sol: 40.3 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→38.63 Å / Num. obs: 27590 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.028 / Rrim(I) all: 0.101 / Net I/σ(I): 13.8 / Num. measured all: 363437
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.6312.82.6491726813510.6550.7662.7591100
8.76-38.6310.30.021223721710.0070.02256.899.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.8data scaling
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PTF

7ptf


Resolution: 1.6→38.63 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 5.922 / SU ML: 0.095 / SU R Cruickshank DPI: 0.0961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1336 4.9 %RANDOM
Rwork0.1807 ---
obs0.1828 26206 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.2 Å2 / Biso mean: 28.473 Å2 / Biso min: 19.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0 Å2
2---2.03 Å20 Å2
3---1.65 Å2
Refinement stepCycle: final / Resolution: 1.6→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 31 216 1857
Biso mean--25.44 40.96 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121791
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161611
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.6382441
X-RAY DIFFRACTIONr_angle_other_deg0.4811.5593753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.2811016
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92610297
X-RAY DIFFRACTIONr_chiral_restr0.0660.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022133
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02384
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 103 -
Rwork0.402 1885 -
all-1988 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 5.8216 Å / Origin y: 16.6851 Å / Origin z: 2.2275 Å
111213212223313233
T0.0577 Å20.0057 Å2-0.0023 Å2-0.0107 Å20.0069 Å2--0.0075 Å2
L1.554 °20.2554 °2-0.1111 °2-1.6275 °2-0.0532 °2--0.8806 °2
S-0.0357 Å °0.0659 Å °0.0011 Å °-0.2664 Å °0.0028 Å °0.0336 Å °0.0747 Å °0.0343 Å °0.0329 Å °

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