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    - PDB-2xyy: De Novo model of Bacteriophage P22 procapsid coat protein -

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    Basic information

    Entry
    Database: PDB / ID: 2xyy
    TitleDe Novo model of Bacteriophage P22 procapsid coat protein
    DescriptorCOAT PROTEIN
    KeywordsVIRUS / ICOSAHEDRAL RECONSTRUCTION
    Specimen sourceENTEROBACTERIA PHAGE P22 / virus
    MethodElectron microscopy (3.8 A resolution / Single particle / Vitreous ice)
    AuthorsChen, D.-H. / Baker, M.L. / Hryc, C.F. / DiMaio, F. / Jakana, J. / Wu, W. / Dougherty, M. / Haase-Pettingell, C. / Schmid, M.F. / Jiang, W. / Baker, D. / King, J.A. / Chiu, W.
    CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 1355-1360

    Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 1355-1360 StrPapers
    Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.
    Dong-Hua Chen / Matthew L Baker / Corey F Hryc / Frank DiMaio / Joanita Jakana / Weimin Wu / Matthew Dougherty / Cameron Haase-Pettingell / Michael F Schmid / Wen Jiang / David Baker / Jonathan A King / Wah Chiu

    DateDeposition: Nov 19, 2010 / Release: Feb 2, 2011 / Last modification: Feb 9, 2011

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    Structure visualization

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    • Biological unit as complete icosahedral assembly
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    • Biological unit as icosahedral pentamer
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    • Biological unit as icosahedral 23 hexamer
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    • Deposited structure unit
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    • Simplified surface model + fitted atomic model
    • EMDB-1824
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    Assembly

    Deposited unit
    A: COAT PROTEIN
    B: COAT PROTEIN
    C: COAT PROTEIN
    D: COAT PROTEIN
    E: COAT PROTEIN
    F: COAT PROTEIN
    G: COAT PROTEIN

    328 kDa, 7 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    327,5737
    Polyers327,5737
    Non-polymers00
    Water0

    Omokage search
    #1
    A: COAT PROTEIN
    B: COAT PROTEIN
    C: COAT PROTEIN
    D: COAT PROTEIN
    E: COAT PROTEIN
    F: COAT PROTEIN
    G: COAT PROTEIN
    x 60
    complete icosahedral assembly / 19.7 MDa, 420 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    19,654,376420
    Polyers19,654,376420
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x60
    Download / Omokage search
    #2idetical with deposited unit in distinct coordinate / icosahedral asymmetric unit / Symmetry operations: (point symmetry)x1
    #3
    A: COAT PROTEIN
    B: COAT PROTEIN
    C: COAT PROTEIN
    D: COAT PROTEIN
    E: COAT PROTEIN
    F: COAT PROTEIN
    G: COAT PROTEIN
    x 5
    icosahedral pentamer / 1.64 MDa, 35 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,637,86535
    Polyers1,637,86535
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: COAT PROTEIN
    B: COAT PROTEIN
    C: COAT PROTEIN
    D: COAT PROTEIN
    E: COAT PROTEIN
    F: COAT PROTEIN
    G: COAT PROTEIN
    x 6
    icosahedral 23 hexamer / 1.97 MDa, 42 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,965,43842
    Polyers1,965,43842
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x6
    PAUidetical with deposited unit in distinct coordinate / icosahedral asymmetric unit, std point frame / Symmetry operations: (transform to point frame)x1

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    Components

    #1polypeptide(L) / COAT PROTEIN / P22 / Source: ENTEROBACTERIA PHAGE P22 (gene. exp.) / References: UniProt: A8CGC7

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    Experimental details

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    Experiment

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

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    Sample preparation

    Assembly of specimenName: BACTERIOPHAGE P22 PROCAPSID / Aggregation state: PARTICLE / Details: BAD MICROGRAPHS WERE EXCLUDED VISUALLY
    Buffer solutionName: 50 MM TRIS PH 7.6, 25 MM NACL, 2MM EDTA
    Sample preparationpH: 7.6 / Sample conc.: 1 mg/ml
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: VITRIFICATION 1 - CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 4.2, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,

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    Electron microscopy imaging

    MicroscopyMicroscope model: JEOL KYOTO-3000SFF / Date: Mar 7, 2008
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 36 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Calibrated magnification: 60000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 500 nm / Cs: 1.6 mm
    Specimen holderTemperature: 4.2 K
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 921
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: EMAN / Number of particles: 23400
    3D reconstructionMethod: FOURIER METHODS / Resolution: 3.8 A / Nominal pixel size: 1.06 A/pix / Actual pixel size: 1.06 A/pix / CTF correction method: EACH PARTICLE
    Details: MAKE3D IN EMAN.N-TERMINAL 9 RESIDUES AND C-TERMINAL 5 RESIDUES WERE NOT MODELED.SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1824.
    Atomic model buildingRef protocol: EM / Ref space: REAL / Target criteria: FSC
    Least-squares processHighest resolution: 3.8 A
    Refine hist #LASTHighest resolution: 3.8 A
    Number of atoms included #LASTProtein: 2912 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2912

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