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    - EMDB-1530: Structure of hexameric DyP from Brevibacterium linens -

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    Basic information

    Entry
    Database: EMDB / ID: 1530
    TitleStructure of hexameric DyP from Brevibacterium linens
    Keywordsprotein complex / hexamer / peroxidase / dye-decolorizing peroxidase / heme containing peroxidase
    SampleStructure of hexameric DyP from Brevibacterium linens
    SourceBrevibacterium linens / bacteria
    Map dataStructure of hexameric DyP from Brevibacterium linens
    Methodsingle particle reconstruction, at 16 A resolution
    AuthorsSutter M / Boehringer D / Gutmann S / Gunther S / Prangishvili D / Loessner MJ / Stetter KO / Weber-Ban E / Ban N
    CitationNat. Struct. Mol. Biol., 2008, 15, 939-947

    Nat. Struct. Mol. Biol., 2008, 15, 939-947 StrPapers
    Structural basis of enzyme encapsulation into a bacterial nanocompartment.
    Markus Sutter / Daniel Boehringer / Sascha Gutmann / Susanne Günther / David Prangishvili / Martin J Loessner / Karl O Stetter / Eilika Weber-Ban / Nenad Ban

    DateDeposition: Jun 24, 2008 / Header (metadata) release: Jun 24, 2008 / Map release: Jun 11, 2009 / Last update: Jun 24, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.18
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.18
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1530.map.gz (map file in CCP4 format, 1025 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    64 pix
    2.8 A/pix
    = 179.2 A
    64 pix
    2.8 A/pix
    = 179.2 A
    64 pix
    2.8 A/pix
    = 179.2 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.8 A
    Density
    Contour Level:0.1 (by author), 0.18 (movie #1):
    Minimum - Maximum-1.38813 - 0.944775
    Average (Standard dev.)-0.00162246 (0.125636)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions646464
    Origin-32-31-32
    Limit313231
    Spacing646464
    CellA=B=C: 179.2 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.82.82.8
    M x/y/z646464
    origin x/y/z0.0000.0000.000
    length x/y/z179.200179.200179.200
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-75-75-74
    NX/NY/NZ150150150
    MAP C/R/S123
    start NC/NR/NS-31-32-32
    NC/NR/NS646464
    D min/max/mean-1.3880.945-0.002

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    Supplemental data

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    Sample components

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    Entire Structure of hexameric DyP from Brevibacterium linens

    EntireName: Structure of hexameric DyP from Brevibacterium linens / Details: monodisperse / Number of components: 1 / Oligomeric State: hexamer
    MassTheoretical: 240 kDa

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    Component #1: protein, dye-decolorizing peroxidase

    ProteinName: dye-decolorizing peroxidase / a.k.a: Dyp / Oligomeric Details: hexamer / Recombinant expression: Yes / Number of Copies: 6
    MassTheoretical: 40 kDa
    SourceSpecies: Brevibacterium linens / bacteria / Strain: M18
    Source (engineered)Expression System: Escherichia coli rosetta / bacteria / image: Escherichia coli
    Vector: pET21a
    External referencesInterPro: InterPro: 006314

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Support filmcarbon coated 200 mesh copper grid
    Staining2% w/v uranyl acetate
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 100000 X (nominal), 100000 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 700 - 1500 nm / Energy filter: Tridiem Gatan
    Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 295 K
    CameraDetector: GATAN ULTRASCAN 1000 (2k x 2k)

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    Image acquisition

    Image acquisitionSampling size: 1.4 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 2878 / Applied symmetry: D3 (2*3 fold dihedral)
    3D reconstructionAlgorithm: angular reconstitution / Software: IMAGIC-5 / CTF correction: Each image / Resolution: 16 A / Resolution method: FSC 3 sigma square root(6)

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