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- EMDB-8486: Bacillus phage PBS1 -

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Basic information

Database: EMDB / ID: 8486
TitleBacillus phage PBS1
SampleBacillus phage PBS1
SourceBacillus phage PBS1 / virus / image: Bacillus subtilis
Map dataBacillus phage PBS1
Methodsingle particle (icosahedral) reconstruction, at 10 Å resolution
AuthorsHua J / Huet A / Lopez CA / Toropova K / Pope WH / Duda RL / Hendrix RW / Conway JF
CitationMBio, 2017, 8

MBio, 2017, 8 Yorodumi Papers
Capsids and Genomes of Jumbo-Sized Bacteriophages Reveal the Evolutionary Reach of the HK97 Fold.
Jianfei Hua / Alexis Huet / Carlos A Lopez / Katerina Toropova / Welkin H Pope / Robert L Duda / Roger W Hendrix / James F Conway

DateDeposition: Nov 29, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Nov 1, 2017 / Last update: Nov 1, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 4.35
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 4.35
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8486.map.gz (map file in CCP4 format, 868328 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
601 pix
2.74 Å/pix.
= 1646.74 Å
601 pix
2.74 Å/pix.
= 1646.74 Å
601 pix
2.74 Å/pix.
= 1646.74 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.74 Å
Contour Level:4.35 (by author), 4.35 (movie #1):
Minimum - Maximum-12.949679 - 23.977083
Average (Standard dev.)0.6991476 (3.3277946)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1646.74 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.742.742.74
M x/y/z601601601
origin x/y/z0.0000.0000.000
length x/y/z1646.7401646.7401646.740
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-12.95023.9770.699

Supplemental data

Sample components

Entire Bacillus phage PBS1

EntireName: Bacillus phage PBS1 / Number of components: 1

Component #1: virus, Bacillus phage PBS1

VirusName: Bacillus phage PBS1 / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Bacillus phage PBS1 / virus / image: Bacillus subtilis
Source (natural)Host Species: Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /
Shell #1Name of element: capsid / Diameter: 1300 Å / T number(triangulation number): 27

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 293 K / Humidity: 90 %

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 5000 nm
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 3000 / Sampling size: 14 microns

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2000
3D reconstructionSoftware: Auto3DEM / Resolution: 10 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot (resolution assessment)

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