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- PDB-7p2w: E.coli GyrB24 with inhibitor LMD92 (EBL2682) -

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Basic information

Entry
Database: PDB / ID: 7p2w
TitleE.coli GyrB24 with inhibitor LMD92 (EBL2682)
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / Gyrase / inhibitor / E.coli / complex
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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / 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-4QR / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsStevenson, C.E.M. / Lawson, D.M. / Maxwell, A.M. / Henderson, S.R. / Kikelj, D. / Durcik, M. / Zega, A. / Zidar, N. / Ilas, J. / Tomasic, T. / Masic, L.P.
Funding support Switzerland, United Kingdom, European Union, Slovenia, 5items
OrganizationGrant numberCountry
Innovative Medicines InitiativeGrant No. 115583 Switzerland
Wellcome Trust110072/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBSRC Institute Strategic Programme Grant United Kingdom
European Communitys Seventh Framework Programme(FP7/2007-2013)European Union
Slovenian Research AgencyP1-0208 Slovenia
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa.
Authors: Cotman, A.E. / Durcik, M. / Benedetto Tiz, D. / Fulgheri, F. / Secci, D. / Sterle, M. / Mozina, S. / Skok, Z. / Zidar, N. / Zega, A. / Ilas, J. / Peterlin Masic, L. / Tomasic, T. / Hughes, D. ...Authors: Cotman, A.E. / Durcik, M. / Benedetto Tiz, D. / Fulgheri, F. / Secci, D. / Sterle, M. / Mozina, S. / Skok, Z. / Zidar, N. / Zega, A. / Ilas, J. / Peterlin Masic, L. / Tomasic, T. / Hughes, D. / Huseby, D.L. / Cao, S. / Garoff, L. / Berruga Fernandez, T. / Giachou, P. / Crone, L. / Simoff, I. / Svensson, R. / Birnir, B. / Korol, S.V. / Jin, Z. / Vicente, F. / Ramos, M.C. / de la Cruz, M. / Glinghammar, B. / Lenhammar, L. / Henderson, S.R. / Mundy, J.E.A. / Maxwell, A. / Stevenson, C.E.M. / Lawson, D.M. / Janssen, G.V. / Sterk, G.J. / Kikelj, D.
History
DepositionJul 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.country
Revision 1.2Jan 31, 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

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8584
Polymers24,1911
Non-polymers6673
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-2 kcal/mol
Surface area9910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.820, 52.620, 81.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 24191.182 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria)
References: UniProt: P0AES6, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-4QR / 2-[[3,4-bis(chloranyl)-5-methyl-1H-pyrrol-2-yl]carbonylamino]-4-[(3-carboxyphenyl)methoxy]-1,3-benzothiazole-6-carboxylic acid


Mass: 520.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H15Cl2N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 34% PEG4K, IOOmMTris pH8, 128mM MgC12

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.65→52.62 Å / Num. obs: 26432 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 18.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.057 / Rrim(I) all: 0.205 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.65-1.6813.72.2941728512630.5810.6392.3821.2
9.04-52.6210.90.04822492070.9990.0140.0537.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kzn

1kzn


Resolution: 1.65→44.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.813 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1221 4.6 %RANDOM
Rwork0.1876 ---
obs0.1892 25156 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.39 Å2 / Biso mean: 24.348 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---1.34 Å20 Å2
3---1.34 Å2
Refinement stepCycle: final / Resolution: 1.65→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 43 202 1819
Biso mean--24.46 36.59 -
Num. residues----204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131705
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171584
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.6382306
X-RAY DIFFRACTIONr_angle_other_deg1.3741.5873650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5685213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5422.3689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73115288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8891511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021952
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02376
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 86 -
Rwork0.316 1808 -
all-1894 -
obs--99.58 %
Refinement TLS params.Method: refined / Origin x: -18.857 Å / Origin y: 1.99 Å / Origin z: -4.021 Å
111213212223313233
T0.0112 Å20.0003 Å20.0113 Å2-0.0108 Å20.0072 Å2--0.0754 Å2
L2.0304 °20.0828 °20.6354 °2-1.3623 °20.2147 °2--1.2867 °2
S0.0002 Å °0.1301 Å °0.0932 Å °-0.048 Å °-0.0355 Å °-0.0395 Å °-0.0631 Å °0.0695 Å °0.0353 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 219
2X-RAY DIFFRACTION1A301 - 302

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