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    - EMDB-1699: Structure of Lactococcal Phage p2 Baseplate and its Mechanism of ... -

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    Basic information

    Entry
    Database: EMDB / ID: 1699
    TitleStructure of Lactococcal Phage p2 Baseplate and its Mechanism of Activation
    Keywordsp2 / baseplate / phage / EM
    SampleP2 baseplate wild-type
    SourceLactococcus phage p2 / virus
    Map dataThis is the ccp4 file of the EM 3D reconstruction of the baseplate of the wild-type p2 bacteriophage. The map is associated to the following PDB entries: PDB: 2WZP: BP closed form PDB: 2X53: BP Activated form C2 PDB: 2X54 + 2X5A: BP Activated form P2
    Methodsingle particle reconstruction, at 22 A resolution
    AuthorsSciara G / Bebeacua C / Bron P / Tremblay D / Ortiz-Lombardia M / Lichiere J / van Heel M / Campanacci V / Moineau S / Cambillau C
    CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 6852-6857

    Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 6852-6857 StrPapers
    Structure of lactococcal phage p2 baseplate and its mechanism of activation.
    Giuliano Sciara / Cecilia Bebeacua / Patrick Bron / Denise Tremblay / Miguel Ortiz-Lombardia / Julie Lichière / Marin van Heel / Valérie Campanacci / Sylvain Moineau / Christian Cambillau

    DateDeposition: Feb 5, 2010 / Header (metadata) release: Mar 10, 2010 / Map release: Mar 10, 2010 / Last update: Feb 5, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.5
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 1.5
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1699.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    4.64 A/pix
    = 593.92 A
    128 pix
    4.64 A/pix
    = 593.92 A
    128 pix
    4.64 A/pix
    = 593.92 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.64 A
    Density
    Contour Level:1.5 (by author), 1.5 (movie #1):
    Minimum - Maximum-7.12447 - 15.0054
    Average (Standard dev.)0.0791262 (0.812704)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin-64-63-64
    Limit636463
    Spacing128128128
    CellA=B=C: 593.92 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.644.644.64
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z593.920593.920593.920
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ000
    NX/NY/NZ121121121
    MAP C/R/S123
    start NC/NR/NS-63-64-64
    NC/NR/NS128128128
    D min/max/mean-7.12415.0050.079

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    Supplemental data

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    Sample components

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    Entire P2 baseplate wild-type

    EntireName: P2 baseplate wild-type / Number of components: 1 / Oligomeric State: Homohexamer
    MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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    Component #1: protein, P2 baseplate

    ProteinName: P2 baseplate / a.k.a: P2 baseplate / Oligomeric Details: Hexamer / Recombinant expression: No / Number of Copies: 6
    SourceSpecies: Lactococcus phage p2 / virus

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    StainingSample was incubated on glow-discharged grid for approximately one minute. 2% uranyl acetate was applied onto the sample and left for about 30 seconds.
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG/UT
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: SPOT SCAN
    LensMagnification: 38000 X (nominal) / Astigmatism: corrected at 200,000 times magnification / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 1500 nm
    Specimen HolderHolder: Room Temperature / Model: OTHER

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    Image acquisition

    Image acquisitionNumber of digital images: 1000 / Sampling size: 2.32 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 9486 / Applied symmetry: C6 (6 fold cyclic)
    3D reconstructionAlgorithm: Exact-filter back projections / Euler angles: IMAGIC / Software: IMAGIC-5 / CTF correction: CCD Images
    Details: Initial map calculated with class averages. Final map calculated after projection matching refinement.
    Resolution: 22 A / Resolution method: FSC 1/2 BIT

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