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- PDB-4mb9: Structure of Streptococcus pneumonia ParE in complex with AZ13102335 -

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Basic information

Entry
Database: PDB / ID: 4mb9
TitleStructure of Streptococcus pneumonia ParE in complex with AZ13102335
ComponentsDNA topoisomerase IV, B subunit
KeywordsISOMERASE/ISOMERASE INHIBITOR / ATP binding / structure-based drug design / antimicrobial / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homologyHistidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 2-Layer Sandwich / Alpha Beta / Chem-28F / :
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOgg, D. / Tucker, J.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Thiazolopyridine Ureas as Novel Antitubercular Agents Acting through Inhibition of DNA Gyrase B.
Authors: Kale, M.G. / Raichurkar, A. / Hameed, S.P. / Waterson, D. / McKinney, D. / Manjunatha, M.R. / Kranthi, U. / Koushik, K. / Jena, L.K. / Shinde, V. / Rudrapatna, S. / Barde, S. / Humnabadkar, ...Authors: Kale, M.G. / Raichurkar, A. / Hameed, S.P. / Waterson, D. / McKinney, D. / Manjunatha, M.R. / Kranthi, U. / Koushik, K. / Jena, L.K. / Shinde, V. / Rudrapatna, S. / Barde, S. / Humnabadkar, V. / Madhavapeddi, P. / Basavarajappa, H. / Ghosh, A. / Ramya, V. / Guptha, S. / Sharma, S. / Vachaspati, P. / Kumar, K.N. / Giridhar, J. / Reddy, J. / Panduga, V. / Ganguly, S. / Ahuja, V. / Gaonkar, S. / Kumar, C.N. / Ogg, D. / Tucker, J.A. / Boriack-Sjodin, P.A. / de Sousa, S.M. / Sambandamurthy, V.K. / Ghorpade, S.R.
History
DepositionAug 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Apr 29, 2015Group: Data collection
Revision 1.3Feb 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: DNA topoisomerase IV, B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0973
Polymers24,6011
Non-polymers4972
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA topoisomerase IV, B subunit
hetero molecules

A: DNA topoisomerase IV, B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1946
Polymers49,2012
Non-polymers9934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2300 Å2
ΔGint-37 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.397, 94.279, 60.535
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 DNA topoisomerase IV, B subunit


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: GA47373 / Gene: SPAR94_0831 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)
References: UniProt: G6TGY9, Isomerases; Other isomerases; Sole sub-subclass for isomerases that do not belong in the other subclasses
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-28F / 1-ethyl-3-{6-(pyrimidin-5-yl)-5-[(3R)-tetrahydrofuran-3-ylmethoxy][1,3]thiazolo[5,4-b]pyridin-2-yl}urea


Mass: 400.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N6O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
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: Oct 12, 2008 / Details: VariMax HF
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→57.92 Å / Num. all: 18301 / Num. obs: 18191 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.53 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.89 % / Rmerge(I) obs: 0.467 / % possible all: 94.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
AMoREphasing
REFMAC5.5.0070refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→57.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.06 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 928 5.1 %RANDOM
Rwork0.19538 ---
obs0.19776 17239 99.26 %-
all-17245 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.595 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.83 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.85→57.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 33 128 1660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021630
X-RAY DIFFRACTIONr_bond_other_d0.0010.021061
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.962215
X-RAY DIFFRACTIONr_angle_other_deg0.94432602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9124.4168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85215271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.487158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02326
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_it0.7911.51013
X-RAY DIFFRACTIONr_mcbond_other0.1861.5425
X-RAY DIFFRACTIONr_mcangle_it1.4221638
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1233617
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4444.5577
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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 67 -
Rwork0.246 1171 -
obs--93.15 %
Refinement TLS params.Method: refined / Origin x: 23.337 Å / Origin y: 32.2447 Å / Origin z: 0.5982 Å
111213212223313233
T0.0097 Å2-0.0013 Å20.007 Å2-0.0154 Å20.0073 Å2--0.0221 Å2
L0.4936 °2-0.2242 °2-0.0283 °2-0.7662 °2-0.1491 °2--0.8638 °2
S-0.0371 Å °-0.0149 Å °-0.0545 Å °0.0235 Å °-0.0097 Å °-0.0057 Å °0.0707 Å °0.0173 Å °0.0469 Å °

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