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    Yorodumi
    - PDB-3h3y: Fitting of the gp6 crystal structure into 3D cryo-EM reconstructi... -

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    Basic information

    Entry
    Database: PDB / ID: 3h3y
    TitleFitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate
    DescriptorBaseplate structural protein Gp6
    KeywordsVIRAL PROTEIN / viral structural protein / Virion
    Specimen sourcebacteriophage T4 / virus
    MethodElectron microscopy (16 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsAksyuk, A.A. / Leiman, P.G. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G.
    CitationStructure, 2009, 17, 800-808

    Structure, 2009, 17, 800-808 StrPapers
    The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate.
    Anastasia A Aksyuk / Petr G Leiman / Mikhail M Shneider / Vadim V Mesyanzhinov / Michael G Rossmann

    DateDeposition: Apr 17, 2009 / Release: May 19, 2009 / Last modification: Jan 19, 2010

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    Assembly

    Deposited unit
    A: Baseplate structural protein Gp6
    B: Baseplate structural protein Gp6
    C: Baseplate structural protein Gp6
    D: Baseplate structural protein Gp6
    E: Baseplate structural protein Gp6
    F: Baseplate structural protein Gp6
    G: Baseplate structural protein Gp6
    H: Baseplate structural protein Gp6
    I: Baseplate structural protein Gp6
    J: Baseplate structural protein Gp6
    K: Baseplate structural protein Gp6
    L: Baseplate structural protein Gp6

    460 kDa, 12 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    459,65912
    Polyers459,65912
    Non-polymers00
    Water0

    Omokage search
    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / Baseplate structural protein Gp6 / Baseplate wedge protein 6 / Fragment: gene product 6 fragment / Mutation: residues 334 to 660 / Source: bacteriophage T4 (gene. exp.) / References: UniProt: P19060

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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    Sample preparation

    Assembly of specimenName: T4 phages treated with 3 M urea / Aggregation state: PARTICLE / Mol wt exp: 220 MDa / Mol wt method: Estimate / Mol wt theo: 220 MDa / Number of components: 1
    ComponentName: A ring of six gp6 dimers in the star-shaped baseplate of bacteriophage T4
    VitrificationCryogen name: ETHANE / Temp: 100 K

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    Electron microscopy imaging

    EM imagingCamera length: 0 mm
    MicroscopyDate: Jan 6, 2002
    Electron gunAccelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3400 nm / Nominal defocus min: 500 nm / Energy filter: FEI
    Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
    Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
    Temperature: 100 K / Tilt angle max: -9999 deg. / Tilt angle min: -9999 deg.
    CameraType: Kodak SO163 film
    EM image scansNumber digital images: 100 / Quant bit size: 8 / Sampling size: 3.93285 microns / Scanner model: ZEISS SCAI
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: COLORES from the SITUS program package / Number of particles: 1965
    EM single particle entitySymmetry type: CYCLIC
    3D reconstructionMethod: back-projection / Software: Spider / Resolution: 16 A / Resolution method: FSC at 0.5 cut-off / Number of particles: 1965 / CTF correction method: Each particle / Euler angles details: theta 45 degrees, phi 180 degrees
    Atomic model buildingSoftware name: COLORES from the SITUS program package
    Number of atoms included #LASTProtein: 31380 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 31380

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