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    - EMDB-5301: Negative Stain reconstruction of the Thermus thermophilus A-ATPas... -

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    Basic information

    Entry
    Database: EMDB / ID: 5301
    TitleNegative Stain reconstruction of the Thermus thermophilus A-ATPase to 23 Angstrom. Opposite Hand to published.
    KeywordsA-ATPase / Thermus thermophilus / ATPase
    SampleThermus thermophilus A-ATPase
    SourceThermus thermophilus / bacteria / thermophilic
    Map dataThis is a negative stain reconstruction of the Thermus thermophilus A-ATPase
    Methodsingle particle reconstruction, at 23 A resolution
    AuthorsBernal RA / Stock D
    CitationStructure, 2004, 12, 1789-1798

    Structure, 2004, 12, 1789-1798 StrPapers
    Three-dimensional structure of the intact Thermus thermophilus H+-ATPase/synthase by electron microscopy.
    Ricardo A Bernal / Daniela Stock

    DateDeposition: Jun 7, 2011 / Header (metadata) release: Jun 9, 2011 / Map release: Jun 9, 2011 / Last update: Jun 7, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.6
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 1.6
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5301.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    3.3 A/pix
    = 422.4 A
    128 pix
    3.3 A/pix
    = 422.4 A
    128 pix
    3.3 A/pix
    = 422.4 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3.3 A
    Density
    Contour Level:1.6 (by author), 1.6 (movie #1):
    Minimum - Maximum-5.80634 - 15.2002
    Average (Standard dev.)1.75237e-09 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin-64-64-64
    Limit636363
    Spacing128128128
    CellA=B=C: 422.4 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z3.33.33.3
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z422.400422.400422.400
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-64-64-64
    NC/NR/NS128128128
    D min/max/mean-5.80615.2000.000

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    Supplemental data

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    Sample components

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    Entire Thermus thermophilus A-ATPase

    EntireName: Thermus thermophilus A-ATPase / Number of components: 1 / Oligomeric State: multi-subunit complex

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    Component #1: cellular-component, ATPase

    Cellular-componentName: ATPase / a.k.a: ATPase / Oligomeric Details: multimer / Recombinant expression: No
    SourceSpecies: Thermus thermophilus / bacteria / thermophilic / Strain: HB8
    Source (natural)Location in cell: membrane

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.02 mg/ml
    Buffer solution: 20 mM Tris, pH 8.0, 2 mM MgCl2, 1 mM EDTA, 0.05% n-dodecyl-beta-D-maltoside, 0.02% NaN3
    pH: 8
    Support film400 mesh 3.05 mm copper grids with a thin layer carbon support
    StainingThree microliters of the T. thermophilus sample, diluted to 0.02 mg/mL, was placed onto the surface of the carbon-coated grid. The sample was blotted off and replaced with 3 microliters of 2% uranyl acetate. The uranyl acetate was blotted away and replaced with 3 microliters of 4% methylamine tungstate. The final drop of methylamine tungstate was blotted away and the grid was left to air dry.
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 12 / Date: Jan 22, 2003
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 42000 X (nominal), 42000 X (calibrated) / Astigmatism: not corrected / Imaging mode: BRIGHT FIELD / Defocus: 1000 nm
    Specimen HolderHolder: side entry single tilt / Model: OTHER / Temperature: 25 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 60 / Number of projections: 12300 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Cross-common lines / Software: MRC Image2000 and Imagic
    CTF correction: no ctf correction done because it was a negative stain reconstruction
    Resolution: 23 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: EMfit / Refinement protocol: rigid body / Target criteria: sumf and number of atoms inside density / Refinement space: REAL
    Details: Protocol: Each chain was fit as a separate rigid body. X-ray coordinates for the bovine alpha3 beta3 and gamma sub-assemblies were manually fitted into the EM density using the program O. The program EMfit (Rossmann et al., 2001) was then used in order to obtain a more quantitative fit.
    Input PDB model: 1E79
    Chain ID: 1E79_A, 1E79_B, 1E79_C, 1E79_D, 1E79_E, 1E79_F, 1E79_G
    Modeling #2Software: EMfit / Refinement protocol: rigid body / Target criteria: sumf and number of atoms inside density / Refinement space: REAL
    Details: Protocol: Each chain was fit as a separate rigid body. X-ray coordinates for the bovine alpha3 beta3 and gamma sub-assemblies were manually fitted into the EM density using the program O. The program EMfit (Rossmann et al., 2001) was then used in order to obtain a more quantitative fit.
    Input PDB model: 1R5Z
    Chain ID: 1R5Z_A, 1R5Z_B, 1R5Z_C
    Modeling #3Software: EMfit / Refinement protocol: rigid body / Target criteria: sumf and number of atoms inside density / Refinement space: REAL
    Details: Protocol: Each chain was fit as a separate rigid body. X-ray coordinates for the bovine alpha3 beta3 and gamma sub-assemblies were manually fitted into the EM density using the program O. The program EMfit (Rossmann et al., 2001) was then used in order to obtain a more quantitative fit.
    Input PDB model: 1C17
    Chain ID: 1C17_A, 1C17_B, 1C17_C, 1C17_D, 1C17_E, 1C17_F, 1C17_G, 1C17_H, 1C17_I, 1C17_J, 1C17_K, 1C17_L

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