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    Yorodumi
    - EMDB-5405: Icosahedral reconstruction of bacteriophage P4 procapsid -

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    Basic information

    Entry
    Database: EMDB / ID: 5405
    TitleIcosahedral reconstruction of bacteriophage P4 procapsid
    Keywordsbacteriophage / P2 / P4 / capsid / procapsid / assembly / size determination / scaffolding protein / triangulation numbers / T=7 dextro / Sid / gpN
    SampleSatellite bacteriophage P4 procapsid
    SourceEscherichia coli / bacteria / Escherichia coli, E. coli /
    Map dataReconstruction of P4 procapsid
    Methodsingle particle (icosahedral) reconstruction, at 8 A resolution
    AuthorsDearborn AD / Laurinmaki P / Chandramouli P / Rodenburg CM / Wang S / Butcher SJ / Dokland T
    CitationJ. Struct. Biol., 2012, 178, 215-224

    J. Struct. Biol., 2012, 178, 215-224 StrPapers
    Structure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations.
    Altaira D Dearborn / Pasi Laurinmaki / Preethi Chandramouli / Cynthia M Rodenburg / Sifang Wang / Sarah J Butcher / Terje Dokland

    DateDeposition: Feb 20, 2012 / Header (metadata) release: Feb 22, 2012 / Map release: May 29, 2012 / Last update: Feb 20, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5405.map.gz (map file in CCP4 format, 39917 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    217 pix
    2.73 A/pix
    = 592.41 A
    217 pix
    2.73 A/pix
    = 592.41 A
    217 pix
    2.73 A/pix
    = 592.41 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.73 A
    Density
    Contour Level:2 (by author), 2 (movie #1):
    Minimum - Maximum-6.67676449 - 11.10193157
    Average (Standard dev.)-2E-8 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions217217217
    Origin-108-108-108
    Limit108108108
    Spacing217217217
    CellA=B=C: 592.41003 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.732.732.73
    M x/y/z217217217
    origin x/y/z0.0000.0000.000
    length x/y/z592.410592.410592.410
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-108-108-108
    NC/NR/NS217217217
    D min/max/mean-6.67711.102-0.000

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    Supplemental data

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    Sample components

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    Entire Satellite bacteriophage P4 procapsid

    EntireName: Satellite bacteriophage P4 procapsid / Number of components: 2 / Oligomeric State: 240 copies of gpN and 60 copies of Sid
    MassTheoretical: 11.268 MDa

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    Component #1: protein, gpN

    ProteinName: gpN / a.k.a: N*, major capsid protein / Oligomeric Details: icosahedral / Recombinant expression: Yes
    MassTheoretical: 9.648 MDa
    SourceSpecies: Escherichia coli / bacteria / / Strain: BL21(DE3)
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pET21

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    Component #2: protein, Sid

    ProteinName: Sid / a.k.a: external scaffolding protein / Oligomeric Details: icosahedral / Recombinant expression: Yes
    MassTheoretical: 1.62 MDa
    SourceSpecies: Escherichia coli / bacteria / E. coli / / Strain: BL21(DE3)
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pET21

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1 mg/ml
    Buffer solution: 10 mM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM MgCl2
    pH: 8
    Support film200 mesh Quantifoil R2/2
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 110 K / Method: Blot for 2 sec before plunging

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Jan 1, 1999
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 3000 nm
    Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 97 K ( 95 - 99 K)
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: OTHER / Sampling size: 4.545 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 2286 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: projection matching, polar Fourier transform / Software: EMAN,AUTO3DEM / CTF correction: Each micrograph / Resolution: 8 A / Resolution method: FSC at 0.25 cutoff

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: Rigid body fitting of individual subsegments
    Input PDB model: 3E8K
    Chain ID: B

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