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- EMDB-1333: The structures of bacteriophages K1E and K1-5 explain processive ... -

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Basic information

Entry
Database: EMDB / ID: 1333
TitleThe structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.
SampleSixfold averaged tail of bacteriophage K1E
SourceEnterobacteria phage K1E / virus / phage K1E tail
Map dataSixfold averaged tail of bacteriophage K1E
Methodsingle particle reconstruction, at 16.4 A resolution
AuthorsLeiman PG / Battisti AJ / Bowman VD / Stummeyer K / Muhlenhoff M / Gerardy-Schahn R / Scholl D / Molineux IJ
CitationJ. Mol. Biol., 2007, 371, 836-849

J. Mol. Biol., 2007, 371, 836-849 StrPapers
The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.
Petr G Leiman / Anthony J Battisti / Valorie D Bowman / Katharina Stummeyer / Martina Mühlenhoff / Rita Gerardy-Schahn / Dean Scholl / Ian J Molineux

DateDeposition: Mar 6, 2007 / Header (metadata) release: Mar 6, 2007 / Map release: Jul 18, 2007 / Last update: Mar 6, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.1
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1333.map.gz (map file in CCP4 format, 21297 KB)
Projections & slices
Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
176 pix
2.98 A/pix
= 524.48 A
176 pix
2.98 A/pix
= 524.48 A
176 pix
2.98 A/pix
= 524.48 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.98 A
Density
Contour Level:1.92, 1.1 (movie #1):
Minimum - Maximum-8.55116 - 9.72964
Average (Standard dev.)3.25921e-10 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions176176176
Origin-88-88-88
Limit878787
Spacing176176176
CellA=B=C: 524.48 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.982.982.98
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z524.480524.480524.480
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-88-88-88
NC/NR/NS176176176
D min/max/mean-8.5519.7300.000

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Supplemental data

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Sample components

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Entire Sixfold averaged tail of bacteriophage K1E

EntireName: Sixfold averaged tail of bacteriophage K1E / Number of components: 1
MassTheoretical: 8 MDa / Experimental: 8 MDa / Measured by: Primary sequence

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Component #1: virus, Enterobacteria phage K1E

VirusName: Enterobacteria phage K1E / a.k.a: phage K1E tail / Class: VIRION / Details: sixfold averaged / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 8 MDa / Experimental: 8 MDa
SpeciesSpecies: Enterobacteria phage K1E / virus / phage K1E tail
Source (natural)Host Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Host category: BACTERIA(EUBACTERIA)

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 50 mM Tris HCl pH 7.5, 100 mM NaCl, 8 mM MgSO4
pH: 7.5
Support filmquantifoil grid
Stainingnone
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 300 K / Humidity: 80 % / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Date: May 10, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/A2 / Illumination mode: SPOT SCAN
LensMagnification: 45000 X (nominal), 47000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3300 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 122 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6105 / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionAlgorithm: weighted back-projection / Software: Spider / CTF correction: Each particle / Resolution: 16.4 A / Resolution method: FSC at 0.4 cut-off

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