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    - EMDB-1637: Proteome organization in a genome-reduced bacterium -Topoisomeras... -

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    Basic information

    Entry
    Database: EMDB / ID: 1637
    TitleProteome organization in a genome-reduced bacterium -Topoisomerase of Mycoplasma pneumoniae -
    KeywordsTopoisomerase / Mycoplasma pneumoniae / single particle
    SampleTopoisomerase from Mycoplasma pneumoniae
    SourceMycoplasma pneumoniae / bacteria
    Map dataMap of topoisomerase
    Methodsingle particle reconstruction, at 21.5 A resolution
    AuthorsKuhner S / vanNoort V / Betts MJ / Leo-Macias A / Batisse C / Rode M / Yamada T / Maier T / Bader S / Beltran-Alvarez P / Castano-Diez D / Chen W-H / Devos D / Guell Cargol M / Norambuena T / Racke I / Rybin V / Schmidt A / Yus E / Aebersold R / Herrmann R / Bottcher B / Frangakis AS / Russell RB / Serrano L / Bork P / Gavin A-C
    CitationScience, 2009, 326, 1235-1240

    Science, 2009, 326, 1235-1240 StrPapers
    Proteome organization in a genome-reduced bacterium.
    Sebastian Kühner / Vera van Noort / Matthew J Betts / Alejandra Leo-Macias / Claire Batisse / Michaela Rode / Takuji Yamada / Tobias Maier / Samuel Bader / Pedro Beltran-Alvarez / Daniel Castaño-Diez / Wei-Hua Chen / Damien Devos / Marc Güell / Tomas Norambuena / Ines Racke / Vladimir Rybin / Alexander Schmidt / Eva Yus / Ruedi Aebersold / Richard Herrmann / Bettina Böttcher / Achilleas S Frangakis / Robert B Russell / Luis Serrano / Peer Bork / Anne-Claude Gavin

    DateDeposition: Aug 3, 2009 / Header (metadata) release: Jun 11, 2010 / Map release: Jun 11, 2010 / Last update: Aug 3, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 6
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 6
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1637.map.gz (map file in CCP4 format, 1025 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    64 pix
    5.2 A/pix
    = 332.8 A
    64 pix
    5.2 A/pix
    = 332.8 A
    64 pix
    5.2 A/pix
    = 332.8 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 5.2 A
    Density
    Contour Level:6 (by author), 6 (movie #1):
    Minimum - Maximum0 - 72.1255
    Average (Standard dev.)0.291584 (2.90852)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions646464
    Origin000
    Limit636363
    Spacing646464
    CellA=B=C: 332.8 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z5.25.25.2
    M x/y/z646464
    origin x/y/z0.0000.0000.000
    length x/y/z332.800332.800332.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-64-64-64
    NX/NY/NZ128128128
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS646464
    D min/max/mean0.00072.1250.292

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    Supplemental data

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    Sample components

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    Entire Topoisomerase from Mycoplasma pneumoniae

    EntireName: Topoisomerase from Mycoplasma pneumoniae / Details: Sample was fixed following the GRAFIX protocol / Number of components: 1

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    Component #1: protein, Topoisomerase

    ProteinName: Topoisomerase / a.k.a: Topoisomerase / Recombinant expression: Yes
    SourceSpecies: Mycoplasma pneumoniae / bacteria
    Source (engineered)Expression System: Mycoplasma pneumoniae / bacteria

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 50mM Hepes, 20% glycerol, 0.075% glutaraldehyde, 100mM NaCl, 1.5 mM MgCl2
    pH: 7.5
    Support film400 mesh copper grid
    StainingGrids were prepared by sandwich negative stain the sample was adsorbed to carbon on mica and floated on 1 % uranyl acetate the carbon was picked up with an uncoated grid then a second piece of carbon, which was also floated on 1% uranyl acetate, was picked up with the same grid sandwiching the sample between the two layers of carbon
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 27500 X (nominal)
    Astigmatism: Corrected at 200000 times magnification on graininess of carbon
    Cs: 2 mm / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
    CameraDetector: GENERIC CCD

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    Image acquisition

    Image acquisitionNumber of digital images: 70 / Sampling size: 14.22 microns / Bit depth: 12
    Details: Images were recorded on CCD, no scanning sampling step size was adjusted to calibrated image size

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 4767 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection matching / Software: IMAGIC, SPIDER, EMAN
    Details: Spider option BP 32F Back Projection - 3D, Sampled, Interpolated in Fourier space
    Resolution: 21.5 A / Resolution method: FSC 0.5

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