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- PDB-6yd9: Ecoli GyrB24 with inhibitor 16a -

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Basic information

Entry
Database: PDB / ID: 6yd9
TitleEcoli GyrB24 with inhibitor 16a
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / DNA gyrase / topoisomerase IV / inhibitor
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 / cytoplasm / cytosol
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-ON2 / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBarancokova, M. / Skok, Z. / Benek, O. / Cruz, C.D. / Tammela, P. / Tomasic, T. / Zidar, N. / Masic, L.P. / Zega, A. / Stevenson, C.E.M. ...Barancokova, M. / Skok, Z. / Benek, O. / Cruz, C.D. / Tammela, P. / Tomasic, T. / Zidar, N. / Masic, L.P. / Zega, A. / Stevenson, C.E.M. / Mundy, J. / Lawson, D.M. / Maxwell, A.M. / Kikelj, D. / Ilas, J.
Funding support Slovenia, Finland, United Kingdom, 6items
OrganizationGrant numberCountry
European Union (EU)EU H2020 ITN-ETN Project INTEGRATE (Project Reference: 642620) Slovenia
European Union (EU)EU FP7 Integrated Project MAREX (Project No. FP7-KBBE-2009-3-245137) Slovenia
Academy of FinlandGrant No. 277001 Finland
Slovenian Research AgencyGrant No. P1-0208 Slovenia
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012523/1 United Kingdom
Wellcome Trust110072/Z/15/Z United Kingdom
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors.
Authors: Skok, Z. / Barancokova, M. / Benek, O. / Cruz, C.D. / Tammela, P. / Tomasic, T. / Zidar, N. / Masic, L.P. / Zega, A. / Stevenson, C.E.M. / Mundy, J.E.A. / Lawson, D.M. / Maxwell, A. / Kikelj, D. / Ilas, J.
History
DepositionMar 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_name_com / entity_src_gen / pdbx_entity_nonpoly / struct_ref / struct_ref_seq
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_nonpoly.name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2Jan 24, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7284
Polymers24,1911
Non-polymers5363
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint3 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.180, 67.143, 68.971
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 (E. coli)
References: UniProt: P0AES6, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-ON2 / N-[6-(3-azanylpropanoylamino)-1,3-benzothiazol-2-yl]-3,4-bis(chloranyl)-5-methyl-1H-pyrrole-2-carboxamide


Mass: 412.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15Cl2N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M MIB pH 4.0; 25 % (w/v) PEG 1500

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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: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→41.18 Å / Num. obs: 25674 / % possible obs: 98.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.202 / Net I/σ(I): 7.2
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1062 / CC1/2: 0.778 / Rrim(I) all: 1.234 / % possible all: 86

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F86

6f86


Resolution: 1.6→35.38 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.002 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0968 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 1346 5.3 %RANDOM
Rwork0.1819 ---
obs0.1836 24258 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.94 Å2 / Biso mean: 20.529 Å2 / Biso min: 11.14 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2---1.75 Å20 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 1.6→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 34 200 1772
Biso mean--27.23 31.58 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131635
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171528
X-RAY DIFFRACTIONr_angle_refined_deg1.591.6422212
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5823537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28222.02484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45915281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4331511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 95 -
Rwork0.26 1543 -
all-1638 -
obs--86.71 %
Refinement TLS params.Method: refined / Origin x: -0.3781 Å / Origin y: -4.7044 Å / Origin z: 12.7656 Å
111213212223313233
T0.0119 Å2-0.0123 Å20.0118 Å2-0.0523 Å2-0.0007 Å2--0.0232 Å2
L0.7492 °2-0.561 °20.219 °2-1.9663 °2-0.3648 °2--1.2494 °2
S-0.0068 Å °0.0088 Å °0.0508 Å °-0.0862 Å °-0.038 Å °-0.2098 Å °0.0392 Å °0.0915 Å °0.0448 Å °

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