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- PDB-4mot: Structure of Streptococcus pneumonia pare in complex with AZ13072886 -

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Basic information

Entry
Database: PDB / ID: 4mot
TitleStructure of Streptococcus pneumonia pare in complex with AZ13072886
ComponentsTopoisomerase IV subunit B
KeywordsISOMERASE/ISOMERASE INHIBITOR / ATP binding / structure-based drug design / antimicrobial / virtual screen / 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-2B7 / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOgg, D. / Boriack-Sjodin, P.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Thiazolopyridone ureas as DNA gyrase B inhibitors: Optimization of antitubercular activity and efficacy.
Authors: Kale, R.R. / Kale, M.G. / Waterson, D. / Raichurkar, A. / Hameed, S.P. / Manjunatha, M.R. / Kishore Reddy, B.K. / Malolanarasimhan, K. / Shinde, V. / Koushik, K. / Jena, L.K. / Menasinakai, ...Authors: Kale, R.R. / Kale, M.G. / Waterson, D. / Raichurkar, A. / Hameed, S.P. / Manjunatha, M.R. / Kishore Reddy, B.K. / Malolanarasimhan, K. / Shinde, V. / Koushik, K. / Jena, L.K. / Menasinakai, S. / Humnabadkar, V. / Madhavapeddi, P. / Basavarajappa, H. / Sharma, S. / Nandishaiah, R. / Mahesh Kumar, K.N. / Ganguly, S. / Ahuja, V. / Gaonkar, S. / Naveen Kumar, C.N. / Ogg, D. / Boriack-Sjodin, P.A. / Sambandamurthy, V.K. / de Sousa, S.M. / Ghorpade, S.R.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Data collection
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Topoisomerase IV subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9982
Polymers24,6011
Non-polymers3971
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.603, 94.571, 61.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Topoisomerase IV subunit B


Mass: 24600.723 Da / Num. of mol.: 1 / Fragment: ATPase domain (UNP Residues 1-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: parE, spar94_0831, spr0756 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q8DQB5, EC: 5.99.1.-
#2: Chemical ChemComp-2B7 / 1-[4-(3-methylbutyl)-5-oxo-6-(pyridin-3-yl)-4,5-dihydro[1,3]thiazolo[5,4-b]pyridin-2-yl]-3-prop-2-en-1-ylurea


Mass: 397.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18-25% Peg4000, 0.2M Ammonium Acetate, 0.1M MIB, pH 7.0, inhibitor soak, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 22, 2008 / Details: mirrors
RadiationMonochromator: Rigaku VariMax mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→26.22 Å / Num. all: 21775 / Num. obs: 20778 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.62 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.05 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 70.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
AMoREphasing
REFMAC5.5.0036refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→26.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.23 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22784 1051 5.1 %RANDOM
Rwork0.18972 ---
obs0.19164 19722 95.17 %-
all-20668 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.297 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 28 113 1626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021540
X-RAY DIFFRACTIONr_bond_other_d0.0010.021016
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.972084
X-RAY DIFFRACTIONr_angle_other_deg0.96932484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4915191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.0724.3764
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37115263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.393158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.011.5950
X-RAY DIFFRACTIONr_mcbond_other0.3051.5398
X-RAY DIFFRACTIONr_mcangle_it1.82721536
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8543590
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6414.5548
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 46 -
Rwork0.22 1030 -
obs--68.19 %
Refinement TLS params.Method: refined / Origin x: 23.2592 Å / Origin y: 32.2294 Å / Origin z: 0.6891 Å
111213212223313233
T0.0063 Å2-0.0023 Å20.0056 Å2-0.027 Å20.0078 Å2--0.0273 Å2
L0.4226 °2-0.1636 °20.0034 °2-1.0367 °2-0.1823 °2--0.8784 °2
S-0.0334 Å °0.0159 Å °-0.0337 Å °0.0064 Å °-0.0279 Å °-0.0478 Å °0.0519 Å °0.0422 Å °0.0613 Å °

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