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- PDB-5l3j: ESCHERICHIA COLI DNA GYRASE B IN COMPLEX WITH BENZOTHIAZOLE-BASED... -

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Basic information

Entry
Database: PDB / ID: 5l3j
TitleESCHERICHIA COLI DNA GYRASE B IN COMPLEX WITH BENZOTHIAZOLE-BASED INHIBITOR
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / Gyrase B / inhibitor / complex / GyrB / Proteros Biostructures / PROTEROS BIOSTRUCTURES GMBH
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 / Ribosomal Protein S5; domain 2 - #10 / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / 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
Chem-6G9 / IODIDE ION / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsGjorgjieva, M. / Tomasic, T. / Barancokova, M. / Katsamakas, S. / Ilas, J. / Montalvao, S. / Tammella, P. / Peterlin Masic, L. / Kikelj, D.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery of Benzothiazole Scaffold-Based DNA Gyrase B Inhibitors.
Authors: Gjorgjieva, M. / Tomasic, T. / Barancokova, M. / Katsamakas, S. / Ilas, J. / Tammela, P. / Peterlin Masic, L. / Kikelj, D.
History
DepositionMay 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,3623
Polymers41,7471
Non-polymers6152
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint0 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.286, 49.585, 70.212
Angle α, β, γ (deg.)90.000, 93.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA gyrase subunit B / Type IIA topoisomerase subunit GyrB


Mass: 41747.016 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 15-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gyrB, Z5190, ECs4634 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AES6, EC: 5.99.1.3
#2: Chemical ChemComp-6G9 / 2-[[2-[[4,5-bis(bromanyl)-1~{H}-pyrrol-2-yl]carbonylamino]-1,3-benzothiazol-6-yl]amino]-2-oxidanylidene-ethanoic acid


Mass: 488.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8Br2N4O4S
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 15-25% PEG3350 / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→70.08 Å / Num. obs: 9437 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.17
Reflection shellResolution: 2.83→3.08 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.446 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→70.08 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.873 / SU B: 39.539 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.47 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 665 7 %RANDOM
Rwork0.258 ---
obs0.2601 8772 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.36 Å2 / Biso mean: 61.018 Å2 / Biso min: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20.81 Å2
2--0.37 Å20 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 2.83→70.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 31 6 2844
Biso mean--77.79 36.26 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192748
X-RAY DIFFRACTIONr_bond_other_d0.0010.021824
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9573741
X-RAY DIFFRACTIONr_angle_other_deg1.40934375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1195358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2124.576118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18815412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6231514
X-RAY DIFFRACTIONr_chiral_restr0.0540.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
LS refinement shellResolution: 2.83→2.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.587 51 -
Rwork0.471 610 -
all-661 -
obs--96.64 %
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)
13.5796-0.4411-1.47412.8628-0.91963.66840.342-0.12020.72610.0423-0.0110.0388-0.7597-0.0227-0.33090.1671-0.00010.0760.328-0.04240.1866-16.49811.78314.434
22.7334-1.20710.98073.4354-0.62211.6111-0.0219-0.0835-0.1526-0.04360.065-0.19650.31420.1065-0.04320.0863-0.00480.0060.4435-0.01280.033111.272-8.0522.736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 222
2X-RAY DIFFRACTION2A223 - 392

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