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    Yorodumi
    - EMDB-1932: Negative stain EM Map of the AAA protein CbbX, a red-type Rubisco... -

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    Basic information

    Entry
    Database: EMDB / ID: 1932
    TitleNegative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R. sphaeroides
    KeywordsAAA+ protein / ATPase / Rubisco activase
    SampleR. sphaeroides CbbX 3D density map.
    SourceRhodobacter sphaeroides / archaea
    Map dataNegative stain EM reconstruction of the R. sphaeroides CbbX hexamer
    Methodsingle particle reconstruction, at 21 A resolution
    AuthorsMueller-Cajar O / Stotz M / Wendler P / Hartl FU / Bracher A / Hayer-Hartl M
    CitationNature, 2011, 479, 194-199

    Nature, 2011, 479, 194-199 StrPapers
    Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
    Oliver Mueller-Cajar / Mathias Stotz / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl

    DateDeposition: Jul 18, 2011 / Header (metadata) release: Aug 26, 2011 / Map release: Nov 3, 2011 / Last update: Jul 18, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.017
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.017
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3zuh
    • Surface level: 0.017
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1932.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    3.31 A/pix
    = 423.68 A
    128 pix
    3.31 A/pix
    = 423.68 A
    128 pix
    3.31 A/pix
    = 423.68 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.31 A
    Density
    Contour Level:0.005 (by emdb), 0.017 (movie #1):
    Minimum - Maximum-0.011328 - 0.197363
    Average (Standard dev.)0.000343572 (0.00533179)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin000
    Limit127127127
    Spacing128128128
    CellA=B=C: 423.68 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.313.313.31
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z423.680423.680423.680
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS128128128
    D min/max/mean-0.0110.1970.000

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    Supplemental data

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    Sample components

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    Entire R. sphaeroides CbbX 3D density map.

    EntireName: R. sphaeroides CbbX 3D density map. / Number of components: 1 / Oligomeric State: Hexamer
    MassTheoretical: 206 kDa

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    Component #1: protein, Rubisco Activase

    ProteinName: Rubisco Activase / a.k.a: CbbX / Oligomeric Details: Hexamer
    Details: The protein is bound to Ribulose-1,5-bisphosphate, ATP and ATPgammaS
    Recombinant expression: Yes / Number of Copies: 6
    MassTheoretical: 206 kDa
    SourceSpecies: Rhodobacter sphaeroides / archaea
    Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
    Vector: pHue
    External referencesGene Ontology: GO: 0005524

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.072 mg/ml
    Buffer solution: 20 mM Tris pH 8.0, 50 mM NaCl, 5mM MgCl2, 1mM Ribulose-1,5-bisphosphate, 1mM ATP/ATPgammaS
    pH: 8
    Support filmplain carbon grid
    StainingGrids with adsorbed protein stained with 2% (w/v) uranyl acetate for 40 seconds.
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 12 / Date: Nov 19, 2010
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 90600 X (nominal), 90600 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected for at 110k magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 260 - 1800 nm
    Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
    CameraDetector: FEI EAGLE (2k x 2k)

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 245 / Applied symmetry: C6 (6 fold cyclic)
    3D reconstructionAlgorithm: angular reconstitution / Software: MRC, IMAGIC, SPIDER / CTF correction: phase flipping, each particle / Resolution: 21 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: rigid body
    Input PDB model: 3SYL
    Modeling #2Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: rigid body
    Input PDB model: 3CF3
    Output model

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