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    Yorodumi
    - EMDB-1678: CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase B... -

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    Basic information

    Entry
    Database: EMDB / ID: 1678
    TitleCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
    KeywordsAAA+ atpase / metallation / tetrapyrroles
    SampleComplex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
    SourceRhodobacter capsulatus / archaea
    Map dataCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
    Methodsingle particle reconstruction, at 14 A resolution
    AuthorsLundqvist J / Elmlund H / Peterson-Wulff R / Elmlund D / Emanuelsson C / Hebert H / Willows R / Hansson M / Lindahl M / Al-Karadaghi S
    CitationStructure, 2010, 18, 354-365

    Structure, 2010, 18, 354-365 StrPapers
    ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
    Joakim Lundqvist / Hans Elmlund / Ragna Peterson Wulff / Lisa Berglund / Dominika Elmlund / Cecilia Emanuelsson / Hans Hebert / Robert D Willows / Mats Hansson / Martin Lindahl / Salam Al-Karadaghi

    DateDeposition: Jan 8, 2010 / Header (metadata) release: Jan 18, 2010 / Map release: Jan 21, 2010 / Last update: Jan 8, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.005
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.005
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1678.map.gz (map file in CCP4 format, 2001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    80 pix
    2.33 A/pix
    = 186.4 A
    80 pix
    2.33 A/pix
    = 186.4 A
    80 pix
    2.33 A/pix
    = 186.4 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.33 A
    Density
    Contour Level:0.005 (by author), 0.005 (movie #1):
    Minimum - Maximum-0.0280966 - 0.0773895
    Average (Standard dev.)0.000822421 (0.00452024)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions808080
    Origin-40-40-40
    Limit393939
    Spacing808080
    CellA=B=C: 186.4 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.332.332.33
    M x/y/z808080
    origin x/y/z0.0000.0000.000
    length x/y/z186.400186.400186.400
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ000
    NX/NY/NZ121121121
    MAP C/R/S123
    start NC/NR/NS-40-40-40
    NC/NR/NS808080
    D min/max/mean-0.0280.0770.001

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    Supplemental data

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    Sample components

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    Entire Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP

    EntireName: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
    Number of components: 1
    MassTheoretical: 660 kDa

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    Component #1: protein, Biosynthetic enzyme

    ProteinName: Biosynthetic enzyme / a.k.a: Mg chelatase / Recombinant expression: Yes
    MassTheoretical: 660 kDa
    SourceSpecies: Rhodobacter capsulatus / archaea
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 8
    VitrificationInstrument: NONE / Cryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2010F
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: OTHER
    LensMagnification: 60000 X (nominal) / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: Eucentric / Model: JEOL

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    Image acquisition

    Image acquisitionNumber of digital images: 6 / Scanner: ZEISS SCAI

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 526 / Number of projections: 17623 / Applied symmetry: C3 (3 fold cyclic)
    3D reconstructionResolution: 14 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Refinement space: REAL
    Input PDB model: 1G8P
    Output model

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