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    - PDB-2y9k: Three-dimensional model of Salmonella's needle complex at subnano... -

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    Basic information

    Entry
    Database: PDB / ID: 2y9k
    TitleThree-dimensional model of Salmonella's needle complex at subnanometer resolution
    DescriptorPROTEIN INVG
    KeywordsPROTEIN TRANSPORT / TYPE III SECRETION SYSTEM / OUTER MEMBRANE RING / SECRETIN FAMILY / C15 FOLD
    Specimen sourceSalmonella enterica subsp. enterica serovar typhimurium / bacteria
    MethodElectron microscopy (8.3 A resolution / Single particle / Vitreous ice)
    AuthorsSchraidt, O. / Marlovits, T.C.
    CitationScience, 2011, 331, 1192-1195

    Science, 2011, 331, 1192-1195 StrPapers
    Three-dimensional model of Salmonella's needle complex at subnanometer resolution.
    Oliver Schraidt / Thomas C Marlovits

    DateDeposition: Feb 15, 2011 / Release: Mar 23, 2011 / Last modification: Mar 20, 2013

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    Assembly

    Deposited unit
    A: PROTEIN INVG
    B: PROTEIN INVG
    C: PROTEIN INVG
    D: PROTEIN INVG
    E: PROTEIN INVG
    F: PROTEIN INVG
    G: PROTEIN INVG
    H: PROTEIN INVG
    I: PROTEIN INVG
    J: PROTEIN INVG
    K: PROTEIN INVG
    L: PROTEIN INVG
    M: PROTEIN INVG
    N: PROTEIN INVG
    O: PROTEIN INVG

    234 kDa, 15 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    234,25615
    Polyers234,25615
    Non-polymers00
    Water0

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

    #1polypeptide(L) / PROTEIN INVG / Fragment: N-TERMINAL DOMAIN, RESIDUES 34-170 / Source: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (gene. exp.) / References: UniProt: P35672

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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: NEEDLE COMPLEX / Aggregation state: PARTICLE
    Specimen supportDetails: CARBON
    VitrificationDetails: LIQUID ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER
    Details: ACUAL MAGNIFICATION AT CCD 112968, CAMERA PIXEL SIZE 15UM, 1.33 ANGSTROM PER PIXEL, DATA COLLECTED SEMI- AUTOMATICALLY USING POINT-2-POINT (DEVELOPED IN-HOUSE)
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 93000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
    Specimen holderTilt angle min: 0 deg.
    CameraType: CCD GATAN 4KX4K
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: IMAGIC, CHIMERA
    3D reconstructionMethod: PROJECTION MATCHING / Resolution: 8.3 A / Actual pixel size: 1.33 A/pix / CTF correction method: EACH CCD FRAME
    Details: RESOLUTION 8.3 ANGSTROM (0.5 FSC), 6.7 ANGSTROM (HALF BIT) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1871. (DEPOSITION ID: 7820).
    Atomic model buildingMethod: RIGID BODY FITTING / Ref space: REAL / Target criteria: CORRELATION
    Least-squares processHighest resolution: 8.3 A
    Refine hist #LASTHighest resolution: 8.3 A
    Number of atoms included #LASTProtein: 16485 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 16485

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