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- PDB-5bod: Crystal structure of Streptococcus pneumonia ParE inhibitor -

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Basic information

Entry
Database: PDB / ID: 5bod
TitleCrystal structure of Streptococcus pneumonia ParE inhibitor
ComponentsDNA topoisomerase 4 subunit B
KeywordsISOMERASE/ISOMERASE INHIBITOR / Inhibitor / 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-TTJ / 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. / 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.Q. / 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

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9022
Polymers24,6011
Non-polymers3011
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9420 Å2
Unit cell
Length a, b, c (Å)73.402, 94.458, 60.967
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 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-TTJ / (2R)-N-[3-(3,5-dimethylphenyl)-1H-pyrazol-5-yl]-1,4-dioxane-2-carboxamide


Mass: 301.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.15 Å3/Da / Density % sol: 42.73 % / 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: 1.5 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.2→42 Å / Num. obs: 12502 / % possible obs: 97.88 % / Redundancy: 11.13 % / Biso Wilson estimate: 24.87 Å2 / Rsym value: 0.151 / Net I/σ(I): 15.54 / Num. measured all: 139184
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
2.095-2.175.860.4273.050.52597.9
2.17-2.2570.465
2.257-2.3590.394
2.359-2.4840.343
2.484-2.6390.294
2.639-2.8430.225
2.843-3.1290.178
3.129-3.5820.15
3.582-4.5120.125
4.5120.068

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EM7

4em7


Resolution: 2.2→42 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1037 10 %
Rwork0.2057 18654 -
obs0.2088 10364 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.56 Å2 / Biso mean: 26.0232 Å2 / Biso min: 16.41 Å2
Refinement stepCycle: final / Resolution: 2.2→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 22 28 1524
Biso mean--29.69 24.69 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021563
X-RAY DIFFRACTIONf_angle_d0.692123
X-RAY DIFFRACTIONf_chiral_restr0.022244
X-RAY DIFFRACTIONf_plane_restr0.002272
X-RAY DIFFRACTIONf_dihedral_angle_d11.048584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25121291206X-RAY DIFFRACTION95
2.2512-2.30750.26891400.26181252X-RAY DIFFRACTION99
2.3075-2.36990.28991340.23291251X-RAY DIFFRACTION100
2.3699-2.43970.28341390.2331258X-RAY DIFFRACTION100
2.4397-2.51840.26641370.25261220X-RAY DIFFRACTION100
2.5184-2.60840.32591390.24211241X-RAY DIFFRACTION100
2.6084-2.71280.2961360.24451254X-RAY DIFFRACTION100
2.7128-2.83620.271390.22361237X-RAY DIFFRACTION100
2.8362-2.98570.25681420.21561248X-RAY DIFFRACTION100
2.9857-3.17270.21121390.22421264X-RAY DIFFRACTION100
3.1727-3.41760.23261420.20421240X-RAY DIFFRACTION100
3.4176-3.76130.20791390.19391228X-RAY DIFFRACTION100
3.7613-4.30510.22161420.17461263X-RAY DIFFRACTION100
4.3051-5.42220.19591370.16231243X-RAY DIFFRACTION100
5.4222-42.01420.19581390.17741249X-RAY DIFFRACTION100

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