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- EMDB-52769: 70S P. gingivalis ribosome W83 strain consensus map -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-52769
Title70S P. gingivalis ribosome W83 strain consensus map
Map data70S P. gingivalis ribosome W83 strain consensus map used to align the composite map
Sample
  • Complex: Porphyromonas gingivalis 70S ribosome (W83 Strain)
KeywordsAntibiotic / Lefamulin / RIBOSOME
Biological speciesPorphyromonas gingivalis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHiregange DG / Bashan A / Yonath A
Funding support Israel, 1 items
OrganizationGrant numberCountry
Other privateTHE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY Israel
CitationJournal: To Be Published
Title: Structural studies of ribosome from an anaerobic Bacteroidete human pathogen Porphyromonas gingivalis
Authors: Hiregange DG / Bashan A / Yonath A
History
DepositionFeb 7, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52769.png

Downloads & links

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Map

FileDownload / File: emd_52769.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S P. gingivalis ribosome W83 strain consensus map used to align the composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 440 pix.
= 370.48 Å		0.84 Å/pix.
x 440 pix.
= 370.48 Å		0.84 Å/pix.
x 440 pix.
= 370.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.025474165 - 0.07393853
Average (Standard dev.)0.00021074431 (±0.0026606224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 370.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52769_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52769_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 : Porphyromonas gingivalis 70S ribosome (W83 Strain)

EntireName: Porphyromonas gingivalis 70S ribosome (W83 Strain)
Components
  • Complex: Porphyromonas gingivalis 70S ribosome (W83 Strain)

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Supramolecule #1: Porphyromonas gingivalis 70S ribosome (W83 Strain)

SupramoleculeName: Porphyromonas gingivalis 70S ribosome (W83 Strain) / type: complex / ID: 1 / Parent: 0
Macromolecule list: #2-#3, #46, #4-#14, #48, #47, #15-#28, #44, #29-#43, #45, #1
Details: 70S ribosome of W83 strain
Source (natural)Organism: Porphyromonas gingivalis (bacteria)

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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: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129576
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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