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- PDB-4lp0: Crystal structure of a topoisomerase ATP inhibitor -

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Basic information

Entry
Database: PDB / ID: 4lp0
TitleCrystal structure of a topoisomerase ATP inhibitor
ComponentsTopoisomerase IV subunit B
KeywordsISOMERASE/ISOMERASE INHIBITOR / protein-inhibitor complex / ATP binding / structure-based drug design / antimicrobial / virtual screen / ATPase domain / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


DNA negative supercoiling 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-1YM / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsBasarab, G.S. / Manchester, J.I. / Bist, S. / Boriack-Sjodin, P.A. / Dangel, B. / Illingsworth, R. / Uria-Nickelsen, M. / Sherer, B.A. / Sriram, S. / Eakin, A.E.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Fragment-to-Hit-to-Lead Discovery of a Novel Pyridylurea Scaffold of ATP Competitive Dual Targeting Type II Topoisomerase Inhibiting Antibacterial Agents.
Authors: Basarab, G.S. / Manchester, J.I. / Bist, S. / Boriack-Sjodin, P.A. / Dangel, B. / Illingworth, R. / Sherer, B.A. / Sriram, S. / Uria-Nickelsen, M. / Eakin, A.E.
History
DepositionJul 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 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

Downloads & links

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Assembly

Deposited unit
A: Topoisomerase IV subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0382
Polymers24,6011
Non-polymers4371
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.875, 94.333, 62.270
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 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, spr0756 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DQB5, Isomerases; Other isomerases; Sole sub-subclass for isomerases that do not belong in the other subclasses
#2: Chemical ChemComp-1YM / 6'-[(ethylcarbamoyl)amino]-4'-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridine-5-carboxylic acid


Mass: 437.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14F3N5O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18-25% Peg4000, 0.2M Ammonium Acetate, 0.1M MIB pH 7, inhibitor soak, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 29, 2007 / Details: monochromator
RadiationMonochromator: Diamond(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.955→62.27 Å / Num. all: 15850 / Num. obs: 15850 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.084 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.95-2.067.30.38620.3861100
2.06-2.197.30.2652.80.2651100
2.19-2.347.10.2293.20.2291100
2.34-2.527.30.1784.10.178199.9
2.52-2.767.30.1275.70.127199.9
2.76-3.097.20.0927.90.092199.8
3.09-3.5770.0611.60.06199.7
3.57-4.376.80.04713.90.047199.7
4.37-6.186.70.0414.80.04199.8
6.18-62.2760.03815.30.038195.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→57.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.263 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1547 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20197 788 5 %RANDOM
Rwork0.16638 ---
obs0.16816 15042 99.5 %-
all-15830 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å20 Å2
2---0.4 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.95→57.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 30 107 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191573
X-RAY DIFFRACTIONr_bond_other_d0.0050.021477
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9672135
X-RAY DIFFRACTIONr_angle_other_deg0.82533400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76724.0367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34815268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.412159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02349
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_it2.2982.069781
X-RAY DIFFRACTIONr_mcbond_other2.2992.064780
X-RAY DIFFRACTIONr_mcangle_it3.0283.071978
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2262.462792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.955→2.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 60 -
Rwork0.21 1123 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 23.082 Å / Origin y: 32.098 Å / Origin z: 0.635 Å
111213212223313233
T0.005 Å2-0.0001 Å20.0047 Å2-0.0244 Å20.0155 Å2--0.0236 Å2
L0.0927 °2-0.1831 °20.0165 °2-0.6931 °2-0.1921 °2--0.5642 °2
S-0.0106 Å °0.0095 Å °-0.0092 Å °-0.0107 Å °-0.0511 Å °-0.0265 Å °0.0294 Å °0.0443 Å °0.0617 Å °

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