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- PDB-4em7: Crystal structure of a topoisomerase ATP inhibitor -

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Basic information

Entry
Database: PDB / ID: 4em7
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-0RA / :
Function and homology information
Biological speciesStreptococcus pneumoniae GA47373 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBoriack-Sjodin, P.A. / Manchester, J.
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 11, 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)24,8672
Polymers24,6011
Non-polymers2661
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.866, 94.569, 60.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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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-0RA / 3-[3-(1H-pyrrolo[2,3-b]pyridin-5-yl)phenyl]propanoic acid


Mass: 266.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 43.07 %
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: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.716→23.83 Å / Num. all: 17156 / Num. obs: 17156 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-27.40.4761.51809024610.476100
2-2.127.40.2922.51718823360.292100
2.12-2.277.40.2183.21616721980.218100
2.27-2.457.40.1634.41525620690.163100
2.45-2.697.40.1315.41395618940.131100
2.69-37.30.09771269117290.097100
3-3.477.30.0778.21118315290.077100
3.47-4.257.20.0649.8954513170.064100
4.25-6.017.10.069.6732810380.06100
6.01-23.836.40.04912.337325850.04997.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→23.83 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2174 / WRfactor Rwork: 0.1888 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8766 / SU B: 5.697 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1492 / SU Rfree: 0.1297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 867 5.1 %RANDOM
Rwork0.1866 ---
obs0.1879 17141 99.87 %-
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: 53.52 Å2 / Biso mean: 25.2291 Å2 / Biso min: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 20 112 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191572
X-RAY DIFFRACTIONr_bond_other_d0.0040.021028
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.9622135
X-RAY DIFFRACTIONr_angle_other_deg0.78232521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7945201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.724.34869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80815271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.35159
X-RAY DIFFRACTIONr_chiral_restr0.0570.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 59 -
Rwork0.2 1088 -
all-1147 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 23.266 Å / Origin y: 32.612 Å / Origin z: 0.553 Å
111213212223313233
T0.0079 Å2-0.0032 Å20.0064 Å2-0.0221 Å20.0062 Å2--0.0142 Å2
L0.2025 °2-0.1587 °20.0676 °2-0.8406 °2-0.067 °2--0.4863 °2
S-0.0234 Å °0.0107 Å °0.0028 Å °0.0048 Å °-0.0259 Å °-0.0379 Å °0.035 Å °0.0022 Å °0.0493 Å °

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