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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
Components
  • (DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)- ...) x 2
  • DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / 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 / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain / Toprim domain profile. / TOPRIM domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6EJ / Chem-94K / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.22 Å
AuthorsBax, B.D. / Chan, P.F. / Stavenger, R.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Authors: 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. / ...Authors: 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.
History
DepositionApr 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Polymers168,4306
Non-polymers2,23316
Water15,187843
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18730 Å2
ΔGint-69 kcal/mol
Surface area55880 Å2
MethodPISA
Unit cell
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-MP61

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Components

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Protein , 1 types, 2 molecules BD

#1: Protein DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A /


Mass: 78125.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: gyrB, SA0005, gyrA, SA0006 / Production host: Escherichia coli (E. coli) / 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 chain DNA (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 method: obtained synthetically / Source: (synth.) synthetic construct
#3: DNA chain DNA (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 method: obtained synthetically / Source: (synth.) synthetic construct

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Non-polymers , 7 types, 859 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-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 / Source method: obtained synthetically / Formula: C20H19ClN2OS
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Chemical ChemComp-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 / Source method: obtained synthetically / Formula: C24H26FN5O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 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 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.22→19.89 Å / Num. obs: 97193 / % possible obs: 99.1 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.053 / Rrim(I) all: 0.124 / Net I/σ(I): 9.5 / Num. measured all: 502194 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.22-2.264.91.1581.10.5380.5531.28799.3
12.16-19.895.90.0290.9990.0130.03175.6

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMAC5.8.0158phasing
RefinementResolution: 2.22→19.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.357 / SU ML: 0.169 / SU R Cruickshank DPI: 0.2322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.192 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 4893 5 %RANDOM
Rwork0.1818 ---
obs0.1841 92297 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.65 Å2 / Biso mean: 43.096 Å2 / Biso min: 18.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---2.13 Å2
Refinement stepCycle: final / Resolution: 2.22→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10580 800 177 851 12408
Biso mean--50.23 47.8 -
Num. residues----1383
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_deg4.53851413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41323.669556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.722152063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7815124
X-RAY DIFFRACTIONr_chiral_restr0.1070.21833
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219171
LS refinement shellResolution: 2.22→2.277 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 365 -
Rwork0.309 6760 -
all-7125 -
obs--99.25 %

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