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    - PDB-1pdj: Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 ba... -

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    Basic information

    Entry
    Database: PDB / ID: 1pdj
    TitleFitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate
    DescriptorBaseplate structural protein Gp27
    KeywordsStructural protein
    Specimen sourceEnterobacteria phage T4 / virus
    MethodElectron microscopy (12 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsKostyuchenko, V.A. / Leiman, P.G. / Chipman, P.R. / Kanamaru, S. / van Raaij, M.J. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G.
    CitationNat. Struct. Biol., 2003, 10, 688-693

    primary. Nat. Struct. Biol., 2003, 10, 688-693 StrPapers
    Three-dimensional structure of bacteriophage T4 baseplate.
    Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann

    #1. Nature, 2002, 415, 553-557
    Structure of the cell-puncturing device of bacteriophage T4
    Kanamaru, S. / Leiman, P.G. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Arisaka, F. / Rossmann, M.G.

    DateDeposition: May 19, 2003 / Release: Sep 9, 2003 / Last modification: Feb 24, 2009

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    Assembly

    Deposited unit
    D: Baseplate structural protein Gp27
    E: Baseplate structural protein Gp27
    F: Baseplate structural protein Gp27

    133 kDa, 3 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    133,2943
    Polyers133,2943
    Non-polymers00
    Water0

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

    #1polypeptide(L) / Baseplate structural protein Gp27 / Hub protein 27 / Source: Enterobacteria phage T4 (gene. exp.) / References: UniProt: P17172

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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 baseplate-tail tube complex / Aggregation state: PARTICLE
    ComponentName: gp27 / Details: trimer
    Buffer solutionName: water
    Sample preparationpH: 7 / Sample conc.: 5 mg/ml
    Specimen supportDetails: holey carbon
    VitrificationDetails: ethane vitrification

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
    Specimen holderTemperature: 70 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163 FILM

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    Processing

    Image selectionSoftware name: situs 2.0/colores / Number of particles: 945
    EM single particle entitySymmetry type: CYCLIC
    3D reconstructionMethod: model based projection matching / Resolution: 12 A / Nominal pixel size: 3.11 A/pix / Actual pixel size: 2.98 A/pix / Magnification calibration: TMV images
    CTF correction method: CTF was corrected for each particle with Wiener filtering
    Details: a modified version of SPIDER was used for the reconstruction
    Atomic model buildingSoftware name: situs 2.0/colores / Ref protocol: laplacian filtered real space / Ref space: REAL / Target criteria: Correlation coefficient maximization
    Number of atoms included #LASTProtein: 1092 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1092

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