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- EMDB-6715: FliF ring of Salmonella flagellar motor -

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Basic information

Entry
Database: EMDB / ID: 6715
TitleFliF ring of Salmonella flagellar motor
SampleFliF ring
SourceSalmonella enterica subsp. enterica serovar typhimurium / bacteria
Map dataFliF ring assembly
Methodsingle particle reconstruction, at 22 Å resolution
AuthorsSuzuki H / Yonekura K / Namba K
CitationJ. Mol. Biol., 2004, 337, 105-113

J. Mol. Biol., 2004, 337, 105-113 StrPapers
Structure of the rotor of the bacterial flagellar motor revealed by electron cryomicroscopy and single-particle image analysis.
Hirofumi Suzuki / Koji Yonekura / Keiichi Namba

DateDeposition: Mar 16, 2017 / Header (metadata) release: Apr 12, 2017 / Map release: Apr 12, 2017 / Last update: Apr 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_6715.map.gz (map file in CCP4 format, 865 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
60 pix
4.8 Å/pix.
= 288. Å
60 pix
4.8 Å/pix.
= 288. Å
60 pix
4.8 Å/pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.8 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-0.36197108 - 1.720217
Average (Standard dev.)0.18555644 (0.41004357)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions606060
Origin-30-30-30
Limit292929
Spacing606060
CellA=B=C: 288 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.84.84.8
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z288.000288.000288.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-30-30-30
NC/NR/NS606060
D min/max/mean-0.3621.7200.186

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Supplemental data

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Sample components

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Entire FliF ring

EntireName: FliF ring / Details: FliF ring oligomer from Salmonella / Number of components: 1
MassTheoretical: 1.6 MDa

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Component #1: protein, FliF ring

ProteinName: FliF ring / Details: FliF ring oligomer from Salmonella / Recombinant expression: No
MassTheoretical: 1.6 MDa
SourceSpecies: Salmonella enterica subsp. enterica serovar typhimurium / bacteria
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: BL21

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 5 mg/ml / pH: 8
Staining8% (w/v) ammonium molybdate, 2% (w/v) trehalose
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: HITACHI EF2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 62500 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 0.8 - 3 nm / Energy filter: Hitachi gamma-type energy filter
Specimen HolderModel: OTHER / Temperature: K ( 93 - 93 K)
CameraDetector: GATAN MULTISCAN

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C26 (26 fold cyclic) / Number of projections: 4800
3D reconstructionSoftware: EMAN / Resolution: 22 Å / Resolution method: FSC 0.5 CUT-OFF

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