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    - PDB-1pdi: Fitting of the C-terminal part of the short tail fibers into the ... -

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    Basic information

    Database: PDB / ID: 1pdi
    TitleFitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate
    DescriptorShort tail fiber 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. J.Mol.Biol., 2001, 314, 1137-1146
    Crystal Structure of a Heat-and Protease-Stable Part of the Bacteriophage T4 Short Tail Fibre
    van Raaij, M.J. / Schoehn, G. / Burda, M.R. / Miller, S.

    #2. To be published Search PubMed
    Structure of the receptor-binding domain of the bacteriophage T4 short tail fibre
    Thomassen, E. / Gielen, G. / Schuetz, M. / Miller, S. / van Raaij, M.J.

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

    Structure visualization

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    Deposited unit
    A: Short tail fiber protein
    B: Short tail fiber protein
    C: Short tail fiber protein
    D: Short tail fiber protein
    E: Short tail fiber protein
    F: Short tail fiber protein
    G: Short tail fiber protein
    H: Short tail fiber protein
    I: Short tail fiber protein
    J: Short tail fiber protein
    K: Short tail fiber protein
    L: Short tail fiber protein
    M: Short tail fiber protein
    N: Short tail fiber protein
    O: Short tail fiber protein
    P: Short tail fiber protein
    Q: Short tail fiber protein
    R: Short tail fiber protein

    537 kDa, 18 molecules
    Theoretical massNumber of molelcules
    (without water)

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


    #1polypeptide(L) / Short tail fiber protein / Protein Gp12, p12 / Source: Enterobacteria phage T4 (gene. exp.) / References: UniProt: P10930

    Experimental details


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

    Sample preparation

    Assembly of specimenName: T4 baseplate-tail tube complex / Aggregation state: PARTICLE
    Details: T4 double mutant, 18-,23-, produces baseplate-tail tube assemblies
    ComponentName: gp12 / Details: trimer
    Buffer solutionName: water
    Sample preparationpH: 7 / Sample conc.: 5 mg/ml
    Specimen supportDetails: holey carbon
    VitrificationDetails: ethane vitrification

    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


    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 particles images
    CTF correction method: CTF correction of individual particles with Wiener filtering
    Details: modifed version of program SPIDER was used for the reconstruction
    Atomic model buildingSoftware name: situs 2.0/colores / Ref protocol: Laplacian transform real space / Ref space: REAL / Target criteria: Correlation Coefficient maximization
    Number of atoms included #LASTProtein: 5004 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 5004

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