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- EMDB-4175: Native encapsulin from Mycobacterium smegmatis -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-4175
TitleNative encapsulin from Mycobacterium smegmatis
Map data
Sample
  • Complex: Cfp29
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsKirykowicz AM / Woodward JD
CitationJournal: To Be Published
Title: Native encapsulin from Mycobacterium smegmatis
Authors: Kirykowicz AM / Woodward JD
History
DepositionNov 27, 2017-
Header (metadata) releaseDec 13, 2017-
Map releaseJul 22, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.79
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.79
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4175.png

Downloads & links

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Map

FileDownload / File: emd_4175.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.84 Å/pix.
x 128 pix.
= 491.52 Å		3.84 Å/pix.
x 128 pix.
= 491.52 Å		3.84 Å/pix.
x 128 pix.
= 491.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.79 / Movie #1: 4.79
Minimum - Maximum-5.071732 - 6.9662967
Average (Standard dev.)-0.00000000145 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 491.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.843.843.84
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z491.520491.520491.520
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-5.0726.966-0.000

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Supplemental data

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Sample components

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Entire : Cfp29

EntireName: Cfp29
Components
  • Complex: Cfp29

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Supramolecule #1: Cfp29

SupramoleculeName: Cfp29 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Icosahedral symmetry imposed
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Location in cell: Cytoplasm
Molecular weightExperimental: 1.7 MDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 8 / Details: 200 mM NaCl, 50 mM Tris-HCl
StainingType: NEGATIVE / Material: Uranyl acetate / Details: Sample washed/blotted with 2% UA and air-dried
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
DetailsNegative stain

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Average exposure time: 0.5 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 1.2 mm / Nominal magnification: 50000
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1024 / Details: Manual picking
Startup modelType of model: OTHER
Details: Initial model generated in EMAN Common Lines with icosahedral symmetry imposed
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Details: EMAN procedure / Number images used: 1024
Initial angle assignmentType: COMMON LINE / Details: EMAN
Final angle assignmentType: PROJECTION MATCHING
Details: 5 iterations of 10 degrees, 5 iterations of 8 degrees, 10 iterations of 5 degrees, and 6 iterations of 3 degrees

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