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- PDB-5boc: Crystal structure of topoisomerase ParE inhibitor -

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Basic information

Entry
Database: PDB / ID: 5boc
TitleCrystal structure of topoisomerase ParE inhibitor
ComponentsDNA topoisomerase 4 subunit BTopoisomerase
KeywordsISOMERASE/ISOMERASE INHIBITOR / Inhibitor / complex / topoisomerase / ParE / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / 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 4 subunit B, Firmicutes/Mollicutes / 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
Chem-TSJ / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTan, Y.W. / Chen, G.Y. / Hung, A.W. / Hill, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Agency for Science, Technology and Research (A*STAR) Joint Council1231B105 Singapore
CitationJournal: To be published
Title: Application of Fragment-based Drug Discovery against DNA GyraseB
Authors: Chen, G.Y. / Ng, F.M. / Tan, Y.W. / Poulsen, A. / Seetoh, W. / Lin, G. / Kang, C. / Then, S.W. / Ahmad, N.H. / Wong, Y.L. / Ng, H. / Chia, B.C.S. / Lau, Q.Y. / Hill, J. / Hung, A.W. / Keller, T.H.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0042
Polymers24,6011
Non-polymers4031
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9470 Å2
Unit cell
Length a, b, c (Å)73.782, 94.802, 60.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DNA topoisomerase 4 subunit B / Topoisomerase / Topoisomerase IV subunit B


Mass: 24600.723 Da / Num. of mol.: 1 / Fragment: UNP residues 1-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Strain: R6 / Gene: parE, spr0756 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DQB5, EC: 5.99.1.3
#2: Chemical ChemComp-TSJ / 3-methyl-4-({3-[3-methyl-5-(trifluoromethyl)phenyl]-1H-pyrazol-5-yl}carbamoyl)benzoic acid


Mass: 403.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16F3N3O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.16 Å3/Da / Density % sol: 43.1 % / Description: plate like
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Acetate, 18-22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.198→47.4 Å / Num. obs: 11160 / % possible obs: 98.76 % / Redundancy: 12.04 % / Biso Wilson estimate: 17.77 Å2 / Rsym value: 0.125 / Net I/av σ(I): 25.27 / Net I/σ(I): 25.27 / Num. measured all: 134367
Reflection shell
Resolution (Å)Highest resolution (Å)Rsym valueDiffraction-IDRejects
2.198-2.2760.28710
2.276-2.3680.23510
2.368-2.4750.21410
2.475-2.6060.18810
2.606-2.7690.16510
2.769-2.9830.13910
2.983-3.2830.12310
3.283-3.7580.11110
3.758-4.7340.09910
4.7340.10210

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Processing

Software
NameVersionClassification
SAINTV8.30Cdata scaling
PHASER2.5.6data processing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
PHENIXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EM7

4em7


Resolution: 2.2→47.4 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1028 9.92 %
Rwork0.1962 18662 -
obs0.2004 10359 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.47 Å2 / Biso mean: 18.1851 Å2 / Biso min: 6.2 Å2
Refinement stepCycle: final / Resolution: 2.2→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 29 33 1538
Biso mean--22.95 17.43 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051590
X-RAY DIFFRACTIONf_angle_d0.8492167
X-RAY DIFFRACTIONf_chiral_restr0.028247
X-RAY DIFFRACTIONf_plane_restr0.005280
X-RAY DIFFRACTIONf_dihedral_angle_d12.517579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2002-2.25140.25881310.22761163129489
2.2514-2.30770.29041270.20741179130695
2.3077-2.370.26711410.20941244138599
2.37-2.43980.24781360.199812641400100
2.4398-2.51850.30111410.222312411382100
2.5185-2.60850.31391350.229812741409100
2.6085-2.7130.27331300.222412361366100
2.713-2.83640.22571410.209912571398100
2.8364-2.98590.26061390.212512671406100
2.9859-3.1730.25661370.228612771414100
3.173-3.41790.24111390.204112321371100
3.4179-3.76170.21831470.186112711418100
3.7617-4.30580.21451390.162212471386100
4.3058-5.42360.17581350.155712501385100
5.4236-47.4120.22851380.177612601398100
Refinement TLS params.Method: refined / Origin x: 23.2438 Å / Origin y: 32.2421 Å / Origin z: 0.3711 Å
111213212223313233
T0.0588 Å20.004 Å20.0024 Å2-0.0639 Å20.0058 Å2--0.0646 Å2
L0.3219 °2-0.0747 °20.0791 °2-0.5633 °2-0.0827 °2--0.4737 °2
S-0.023 Å °-0.0016 Å °-0.0064 Å °-0.0055 Å °-0.0003 Å °0.0152 Å °0.0596 Å °0.0259 Å °-0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA17 - 226
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allD1 - 42

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