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    Yorodumi
    - 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
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    • Surface view colored by cylindrical radius
    • Surface level: 1.1
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1333.map.gz (map file in CCP4 format, 21297 KB)
    Projections & slicesSize of images:
    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 / / 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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