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- PDB-36up: S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA -

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Basic information

Entry
Database: PDB / ID: 36up
TitleS. aureus DNA Gyrase in complex with OSUAB-0284 and DNA
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
  • DNA Gyrase subunit B, DNA Gyrase subunit A
KeywordsDNA BINDING PROTEIN/DNA / Topoisomerase / NBTI / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology: / : / DNA / DNA (> 10)
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsWheat, C.T. / Bell, C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI173072 United States
CitationJournal: To Be Published
Title: In vitro and in vivo activity of OSUAB-0284, a preclinical candidate for Staphylococcus aureus infection
Authors: Mann, C.A. / West, J.C. / Cassel, S.R. / Wheat, C.T. / Landgraf, A.D. / Tomkovicz, J.V. / Zhao, X. / Eaton, S. / Dellos-Nolan, S. / Baldridge, I. / Srivastava, P. / Kennedy-Mendez, A. / ...Authors: Mann, C.A. / West, J.C. / Cassel, S.R. / Wheat, C.T. / Landgraf, A.D. / Tomkovicz, J.V. / Zhao, X. / Eaton, S. / Dellos-Nolan, S. / Baldridge, I. / Srivastava, P. / Kennedy-Mendez, A. / Pillar, C.M. / Hufnagel, D.A. / Kebriaei, R. / Bell, C.E. / Wozniak, D.J. / Yalowich, J.C. / Mitton-Fry, M.J.
History
DepositionJul 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)169,2007
Polymers168,6044
Non-polymers5963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: DNA chain DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 6135.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein DNA Gyrase subunit B, DNA Gyrase subunit A


Mass: 78166.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Production host: Escherichia coli BL21 (bacteria)
#3: Chemical ChemComp-A1DL2 / 6-[({(2r,5S)-2-[(1S)-2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)-1-hydroxyethyl]-1,3-dioxan-5-yl}amino)methyl]-2H-pyrazino[2,3-b][1,4]oxazin-3(4H)-one


Mass: 486.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23FN6O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53000 / Symmetry type: POINT
RefinementHighest resolution: 2.75 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00511782
ELECTRON MICROSCOPYf_angle_d1.07616046
ELECTRON MICROSCOPYf_dihedral_angle_d15.9191940
ELECTRON MICROSCOPYf_chiral_restr0.0691804
ELECTRON MICROSCOPYf_plane_restr0.0151966

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