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- EMDB-32614: Overall structure of Helicobacter pylori bacteriophage KHP30 -

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Basic information

Entry
Database: EMDB / ID: EMD-32614
TitleOverall structure of Helicobacter pylori bacteriophage KHP30
Map data
Sample
  • Virus: Helicobacter phage KHP (virus)
Biological speciesHelicobacter phage KHP (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsKamiya R / Uchiyama J / Matsuzaki S / Murata K / Iwasaki K / Miyazaki N
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K18521 Japan
Japan Society for the Promotion of Science (JSPS)18K06154 Japan
CitationJournal: To Be Published
Title: Tail structure of Helicobacter pylori bacteriophage KHP30 by single particle cryo-electron microscopy
Authors: Kamiya R / Uchiyama J / Matsuzaki S / Murata K / Iwasaki K / Miyazaki N
History
DepositionJan 15, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32614.png

Downloads & links

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Map

FileDownload / File: emd_32614.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.18 Å/pix.
x 350 pix.
= 1113. Å		3.18 Å/pix.
x 350 pix.
= 1113. Å		3.18 Å/pix.
x 350 pix.
= 1113. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.1360957 - 0.28809127
Average (Standard dev.)0.0023875905 (±0.016950803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 1113.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Helicobacter phage KHP

EntireName: Helicobacter phage KHP (virus)
Components
  • Virus: Helicobacter phage KHP (virus)

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Supramolecule #1: Helicobacter phage KHP

SupramoleculeName: Helicobacter phage KHP / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 1208236 / Sci species name: Helicobacter phage KHP / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: Head / Diameter: 700.0 Å / T number (triangulation number): 9

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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: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.5 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 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

Particle selectionNumber selected: 32655
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 27422
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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