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    ID:- Chain:- Residue:- Atom:-
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    Yorodumi
    - EMDB-5245: Mm-cpn rls with ATP -

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    Basic information

    Entry
    Database: EMDB / ID: 5245
    TitleMm-cpn rls with ATP
    KeywordsMm-cpn / maripaludis / chaperonin
    SampleMm-cpn rls with ATP
    SourceMethanococcus maripaludis / archaea
    Map dataThis is the density map of Mm-cpn rls with ATP state
    Methodsingle particle reconstruction, at 6.7 A resolution
    AuthorsDouglas NR / Reissmann S / Zhang J / Chen B / Jakana J / Kumar R / Chiu W / Frydman J
    CitationCell, 2011, 144, 240-252

    Cell, 2011, 144, 240-252 StrPapers
    Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber.
    Nicholai R Douglas / Stefanie Reissmann / Junjie Zhang / Bo Chen / Joanita Jakana / Ramya Kumar / Wah Chiu / Judith Frydman

    DateDeposition: Oct 29, 2010 / Header (metadata) release: Jan 24, 2011 / Map release: Jan 24, 2011 / Last update: Oct 29, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.28
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 0.28
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-3izi
    • Surface level: 0.28
    • Imaged by UCSF CHIMERA
    • Download
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5245.map.gz (map file in CCP4 format, 27649 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    192 pix
    1.33 A/pix
    = 255.36 A
    192 pix
    1.33 A/pix
    = 255.36 A
    192 pix
    1.33 A/pix
    = 255.36 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.33 A
    Density
    Contour Level:0.28 (by author), 0.28 (movie #1):
    Minimum - Maximum-0.36587054 - 0.74392915
    Average (Standard dev.)0.01685881 (0.07132065)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions192192192
    Origin-96-96-96
    Limit959595
    Spacing192192192
    CellA=B=C: 255.36002 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.331.331.33
    M x/y/z192192192
    origin x/y/z0.0000.0000.000
    length x/y/z255.360255.360255.360
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-96-96-96
    NC/NR/NS192192192
    D min/max/mean-0.3660.7440.017

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    Supplemental data

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    Sample components

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    Entire Mm-cpn rls with ATP

    EntireName: Mm-cpn rls with ATP / Number of components: 1 / Oligomeric State: 16-mer
    MassTheoretical: 900 kDa / Experimental: 900 kDa

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    Component #1: protein, chaperonin

    ProteinName: chaperonin / a.k.a: Mm-cpn / Recombinant expression: Yes
    MassTheoretical: 900 kDa / Experimental: 900 kDa
    SourceSpecies: Methanococcus maripaludis / archaea
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Details: Vitrification instrument: vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 3200FSC
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
    LensImaging mode: BRIGHT FIELD
    Specimen HolderHolder: Gatan side entry / Model: GATAN LIQUID NITROGEN
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image acquisition

    Image acquisitionScanner: OTHER

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    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: D8 (2*8 fold dihedral)
    3D reconstructionSoftware: EMAN / Resolution: 6.7 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Output model

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