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- EMDB-77872: S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-77872
TitleS. aureus DNA Gyrase in complex with OSUAB-0284 and DNA
Map data
Sample
  • Complex: S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA
    • DNA: 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')
    • Protein or peptide: DNA Gyrase subunit B, DNA Gyrase subunit A
  • Ligand: 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
  • Ligand: MANGANESE (II) ION
KeywordsTopoisomerase / NBTI / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsWheat CT / Bell CE
Funding support United States, 1 items
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 CA / West JC / Cassel SR / Wheat CT / Landgraf AD / Tomkovicz JV / Zhao X / Eaton S / Dellos-Nolan S / Baldridge I / Srivastava P / Kennedy-Mendez A / Pillar CM / Hufnagel DA / Kebriaei ...Authors: Mann CA / West JC / Cassel SR / Wheat CT / Landgraf AD / Tomkovicz JV / Zhao X / Eaton S / Dellos-Nolan S / Baldridge I / Srivastava P / Kennedy-Mendez A / Pillar CM / Hufnagel DA / Kebriaei R / Bell CE / Wozniak DJ / Yalowich JC / Mitton-Fry MJ
History
DepositionJul 1, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77872.png

Downloads & links

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Map

FileDownload / File: emd_77872.map.gz / Format: CCP4 / Size: 65.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 258 pix.
= 219.816 Å		0.85 Å/pix.
x 258 pix.
= 219.816 Å		0.85 Å/pix.
x 258 pix.
= 219.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-0.001760599 - 1.9754974
Average (Standard dev.)0.0022621811 (±0.034739748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions258258258
Spacing258258258
CellA=B=C: 219.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_77872_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77872_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA

EntireName: S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA
Components
  • Complex: S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA
    • DNA: 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')
    • Protein or peptide: DNA Gyrase subunit B, DNA Gyrase subunit A
  • Ligand: 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
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA

SupramoleculeName: S. aureus DNA Gyrase in complex with OSUAB-0284 and DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)

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Macromolecule #1: DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP...

MacromoleculeName: 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')
type: dna / ID: 1 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.135955 KDa
SequenceString:
(DA)(DG)(DC)(DC)(DG)(DT)(DA)(DG)(DG)(DG) (DC)(DC)(DC)(DT)(DA)(DC)(DG)(DG)(DC)(DT)

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Macromolecule #2: DNA Gyrase subunit B, DNA Gyrase subunit A

MacromoleculeName: DNA Gyrase subunit B, DNA Gyrase subunit A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)
Molecular weightTheoretical: 78.166055 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: GMDVASLPGK LADCSSKSPE ECEIFLVEGD SAGGSTKSGR DSRTQAILPL RGKILNVEKA RLDRILNNNE IRQMITAFGT GIGGDFDLA KARYHKIVIM TDADVDGAHI RTLLLTFFYR FMRPLIEAGY VYIAQPPTGY KGLGEMNADQ LWETTMNPEH R ALLQVKLE ...String:
GMDVASLPGK LADCSSKSPE ECEIFLVEGD SAGGSTKSGR DSRTQAILPL RGKILNVEKA RLDRILNNNE IRQMITAFGT GIGGDFDLA KARYHKIVIM TDADVDGAHI RTLLLTFFYR FMRPLIEAGY VYIAQPPTGY KGLGEMNADQ LWETTMNPEH R ALLQVKLE DAIEADQTFE MLMGDVVENR RQFIEDNAVY ANLDFAELPQ SRINERNITS EMRESFLDYA MSVIVARALP DV RDGLKPV HRRILYGLNE QGMTPDKSYK KSARIVGDVM GKYHPHGDSS IYEAMVRMAQ DFSYRYPLVD GQGNFGSMDG DGA AAMRFT EARMTKITLE LLRDINKDTI DFIDNYDGNE REPSVLPARF PNLLANGASG IAVGMATNIP PHNLTELING VLSL SKNPD ISIAELMEDI EGPDFPTAGL ILGKSGIRRA YETGRGSIQM RSRAVIEERG GGRQRIVVTE IPFQVNKARM IEKIA ELVR DKKIDGITDL RDETSLRTGV RVVIDVRKDA NASVILNNLY KQTPLQTSFG VNMIALVNGR PKLINLKEAL VHYLEH QKT VVRRRTQYNL RKAKDRAHIL EGLRIALDHI DEIISTIRES DTDKVAMESL QQRFKLSEKQ AQAILDMRLR RLTGLER DK IEAEYNELLN YISELETILA DEEVLLQLVR DELTEIRDRF GDDRRTEIQL G

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Macromolecule #3: 6-[({(2r,5S)-2-[(1S)-2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)...

MacromoleculeName: 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
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1DL2
Molecular weightTheoretical: 486.453 Da

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 53000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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