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- PDB-5npp: 2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYR... -

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Basic information

Entry
Database: PDB / ID: 5npp
Title2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYRASE AND DNA
DescriptorDNA gyrase subunit B
DNA gyrase subunit A/DNA Complex
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR
Specimen sourceStaphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌
Synthetic construct
MethodX-ray diffraction (2.22 Å resolution)
AuthorsBax, B.D. / Chan, P.F. / Stavenger, R.A.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, E4492-E4500

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E4492-E4500 StrPapers
Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Chan, P.F. / Germe, T. / Bax, B.D. / Huang, J. / Thalji, R.K. / Bacque, E. / Checchia, A. / Chen, D. / Cui, H. / Ding, X. / Ingraham, K. / McCloskey, L. / Raha, K. / Srikannathasan, V. / Maxwell, A. / Stavenger, R.A.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 18, 2017 / Release: Jul 12, 2017

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Assembly

Deposited unit
B: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
E: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
A: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
F: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
C: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,66322
Polyers168,4306
Non-polymers2,23316
Water15,187843
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)18730
ΔGint (kcal/M)-69
Surface area (Å2)55880
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)92.850, 92.850, 409.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP 61

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Components

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Polypeptide(L) , 1 types, 2 molecules BD

#1: Polypeptide(L)DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A


Mass: 78125.000 Da / Num. of mol.: 2 / Source: (gene. exp.) Staphylococcus aureus / References: UniProt: P66937, UniProt: Q99XG5, EC: 5.99.1.3

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DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)- ... , 2 types, 4 molecules EFAC

#2: DNA chainDNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 2451.630 Da / Num. of mol.: 2 / Source: (synth.) synthetic construct
#3: DNA chainDNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 3638.379 Da / Num. of mol.: 2 / Source: (synth.) synthetic construct

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Non-polymers , 7 types, 859 molecules

#4: ChemicalChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Formula: Mn
#5: ChemicalChemComp-94K / ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide


Mass: 370.896 Da / Num. of mol.: 2 / Formula: C20H19ClN2OS
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Formula: C3H8O3
#7: ChemicalChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na
#8: ChemicalChemComp-DMS / DIMETHYL SULFOXIDE / DMSO (precipitant for crystallization) *YM


Mass: 78.133 Da / Num. of mol.: 1 / Formula: C2H6OS
#9: ChemicalChemComp-6EJ / (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one


Mass: 451.493 Da / Num. of mol.: 1 / Formula: C24H26FN5O3
#10: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 3.1 / Density percent sol: 60.35
Crystal growTemp: 293 K / Method: MICROBATCH / Details: 7-11% PEG 5000 MME, 130-190 mM Bis-Tris pH 6.2

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: DIAMOND BEAMLINE I04-1 / Synchrotron site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Collection date: Feb 13, 2012
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionD resolution high: 2.22 Å / D resolution low: 19.89 Å / Number obs: 97193 / CC half: 0.997 / Rmerge I obs: 0.111 / Rpim I all: 0.053 / Rrim I all: 0.124 / NetI over sigmaI: 9.5 / Number measured all: 502194 / Redundancy: 5.2 / Scaling rejects: 0 / Percent possible obs: 99.1
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsCC halfRpim I allRrim I allRedundancyPercent possible all
1.1582.2202.2601.10.5380.5531.2874.90099.300
0.02912.16019.8900.9990.0130.0315.90075.600

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMAC5.8.0158phasing
RefineCorrelation coeff Fo to Fc: 0.964 / Correlation coeff Fo to Fc free: 0.938 / Details: U VALUES : REFINED INDIVIDUALLY / Overall SU B: 7.357 / Overall SU ML: 0.169 / Overall SU R Cruickshank DPI: 0.2322 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.232 / Overall ESU R Free: 0.192
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso max: 123.65 Å2 / B iso mean: 43.096 Å2 / B iso min: 18.38 Å2 / Aniso B11: -0.66 Å2 / Aniso B12: -0.33 Å2 / Aniso B13: 0 Å2 / Aniso B22: -0.66 Å2 / Aniso B23: 0 Å2 / Aniso B33: 2.13 Å2
Least-squares processR factor R free: 0.2269 / R factor R work: 0.1818 / R factor obs: 0.1841 / Highest resolution: 2.22 Å / Lowest resolution: 19.89 Å / Number reflection R free: 4893 / Number reflection obs: 92297 / Percent reflection R free: 5 / Percent reflection obs: 99.11
Refine hist #finalHighest resolution: 2.22 Å / Lowest resolution: 19.89 Å / B iso mean ligand: 50.23 / B iso mean solvent: 47.8 / Number residues total: 1383
Number of atoms included #finalProtein: 10580 / Nucleic acid: 800 / Ligand: 177 / Solvent: 851 / Total: 12408
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01912356
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.91216903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5385.0001413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41323.669556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72215.0002063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.78015.000124
X-RAY DIFFRACTIONr_chiral_restr0.1070.2001833
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219171
Refine LS shellHighest resolution: 2.22 Å / R factor R free: 0.323 / R factor R free error: 0 / R factor R work: 0.309 / Lowest resolution: 2.277 Å / Number reflection R free: 365 / Number reflection R work: 6760 / Number reflection all: 7125 / Total number of bins used: 20 / Percent reflection obs: 99.25

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