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

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Basic information

Entry
Database: PDB / ID: 4emv
TitleCrystal structure of a topoisomerase ATP inhibitor
ComponentsDNA topoisomerase IV, B subunit
KeywordsISOMERASE/ISOMERASE INHIBITOR / protein-inhibitor complex / ATP binding / structure-based drug design / antimicrobial / virtual screen / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homologyHistidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 2-Layer Sandwich / Alpha Beta / Chem-0R9 / :
Function and homology information
Biological speciesStreptococcus pneumoniae GA47373 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBoriack-Sjodin, P.A. / Manchester, J. / Hull, K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Discovery of a novel azaindole class of antibacterial agents targeting the ATPase domains of DNA gyrase and Topoisomerase IV.
Authors: Manchester, J.I. / Dussault, D.D. / Rose, J.A. / Boriack-Sjodin, P.A. / Uria-Nickelsen, M. / Ioannidis, G. / Bist, S. / Fleming, P. / Hull, K.G.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 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)25,0452
Polymers24,6011
Non-polymers4441
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.297, 94.920, 61.247
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 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 GA47373 (bacteria)
Gene: ParE, 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-0R9 / 5-{2-(ethylcarbamoyl)-4-[3-(trifluoromethyl)-1H-pyrazol-1-yl]-1H-pyrrolo[2,3-b]pyridin-5-yl}pyridine-3-carboxylic acid


Mass: 444.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15F3N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: inhibitor soak / pH: 7
Details: 18-25% Peg4000, 0.2M Ammonium Acetate, 0.1M MIB pH 7, inhibitor soak, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 21, 2011 / 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: 1.7→31.45 Å / Num. all: 23839 / Num. obs: 23839 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rsym value: 0.103 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.797.10.3442.12459934460.344100
1.79-1.97.20.2432328832570.24100
1.9-2.037.20.16542207930770.165100
2.03-2.197.20.1235.22053128580.123100
2.19-2.47.20.1015.71909226510.101100
2.4-2.697.20.1035.61723623980.103100
2.69-3.17.20.11551513521160.115100
3.1-3.87.10.0926.51306018330.092100
3.8-5.386.80.078.7973314280.0799.5
5.38-27.0826.10.0748.147487750.07494

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→31.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2366 / WRfactor Rwork: 0.2005 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8728 / SU B: 1.9 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1103 / SU Rfree: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1217 5.1 %RANDOM
Rwork0.1894 ---
obs0.1911 23811 99.67 %-
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 max: 47.64 Å2 / Biso mean: 20.758 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 32 178 1716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191616
X-RAY DIFFRACTIONr_bond_other_d0.0010.021046
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.9762199
X-RAY DIFFRACTIONr_angle_other_deg0.77532563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8385204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36224.34869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61915275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.298159
X-RAY DIFFRACTIONr_chiral_restr0.0580.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 97 -
Rwork0.218 1527 -
all-1624 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 23.176 Å / Origin y: 32.227 Å / Origin z: 0.704 Å
111213212223313233
T0.0042 Å2-0.0037 Å20.0036 Å2-0.0198 Å20.0079 Å2--0.0199 Å2
L0.2731 °2-0.1717 °2-0.0937 °2-0.6424 °2-0.1028 °2--0.5659 °2
S-0.0267 Å °0.0046 Å °-0.0191 Å °0.0084 Å °-0.018 Å °-0.0327 Å °0.0257 Å °0.0216 Å °0.0448 Å °

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