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    Yorodumi
    - EMDB-1356: Structural basis for the PufX-mediated dimerization of bacterial ... -

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    Basic information

    Entry
    Database: EMDB / ID: 1356
    TitleStructural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
    SampleCore complex of Rhodobacter veldkampii
    SourceRhodobacter veldkampii / archaea
    Map data3D map file of Rhobacter veldkampii LH1-RC obtained by cryoEM and low-pass filtered at a resolution of 11 angstroems
    Methodsingle particle reconstruction, at 12 A resolution
    AuthorsBusselez J / Cottevieille M / Cuniasse P / Boisset N / Levy D
    CitationStructure, 2007, 15, 1674-1683

    Structure, 2007, 15, 1674-1683 StrPapers
    Structural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
    Johan Busselez / Magali Cottevieille / Philippe Cuniasse / Francesca Gubellini / Nicolas Boisset / Daniel Lévy

    DateDeposition: Apr 27, 2007 / Header (metadata) release: May 3, 2007 / Map release: Jan 7, 2008 / Last update: Apr 27, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0095
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.0095
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1356.map.gz (map file in CCP4 format, 6099 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    116 pix
    1.95 A/pix
    = 226.2 A
    116 pix
    1.95 A/pix
    = 226.2 A
    116 pix
    1.95 A/pix
    = 226.2 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.95 A
    Density
    Contour Level:0.00493, 0.0095 (movie #1):
    Minimum - Maximum-0.0353536 - 0.0627238
    Average (Standard dev.)3.79676e-05 (0.00326315)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions116116116
    Origin-58-58-58
    Limit575757
    Spacing116116116
    CellA=B=C: 226.2 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.951.951.95
    M x/y/z116116116
    origin x/y/z0.0000.0000.000
    length x/y/z226.200226.200226.200
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-64-64-64
    NX/NY/NZ128128128
    MAP C/R/S123
    start NC/NR/NS-58-58-58
    NC/NR/NS116116116
    D min/max/mean-0.0350.0630.000

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    Supplemental data

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    Sample components

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    Entire Core complex of Rhodobacter veldkampii

    EntireName: Core complex of Rhodobacter veldkampii / Oligomeric State: monomers / Number of components: 1
    MassTheoretical: 300 kDa

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    Component #1: protein, core complex of Rba. veldkampii

    ProteinName: core complex of Rba. veldkampii / a.k.a: LH1-RC of Rba. veldkampii / Oligomeric Details: Monomer / Recombinant expression: No / Number of Copies: 1
    MassExperimental: 300 kDa
    SourceSpecies: Rhodobacter veldkampii / archaea / Strain: DSM 11550

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1.5 mg/ml
    Buffer solution: Glycine-glycine 50 mM, NaCl 200 mM, DOTM 0.1 %
    pH: 7.6
    StainingCRYOEM : 4 microL were applied on a Lacey Formwar grid.
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Method: Manual single-sided blotting / Details: Vitrification instrument: manual plunger

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2010F / Date: Jun 1, 2005 / Details: low-dose illumination
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 45000 X (nominal), 45000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1870 - 3460 nm
    Specimen HolderHolder: Gatan / Model: GATAN LIQUID NITROGEN / Temperature: K ( 93 - 94 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 74 / Scanner: OTHER / Bit depth: 8 / Details: Scanner model : Nikon Coolscan 8000ED

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 27000
    Details: Particles were semi-automatically selected using Boxer algorithm of EMAN software
    Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: projection matching / Software: SPIDER / CTF correction: Wiener filtration on volumes / Resolution: 12 A / Resolution method: FSC 0.5
    FSC plot (resolution assessment)

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