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- EMDB-10005: Native bacterioferritin from Mycobacterium smegmatis -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-10005
TitleNative bacterioferritin from Mycobacterium smegmatis
Map dataNative bacterioferritin from Mycobacterium smegmatis
Sample
  • Complex: Bacterioferritin; ferritin family protein
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsKirykowicz AM / Woodward JD
Funding support South Africa, 1 items
OrganizationGrant numberCountry
National Research Foundation in South Africa92556 South Africa
CitationJournal: To Be Published
Title: Structural pipeline for the investigation of Mycobacterial protein complexes involved in the stationary phase stress response
Authors: Kirykowicz AM / Woodward JD
History
DepositionMay 27, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseMay 6, 2020-
UpdateMay 6, 2020-
Current statusMay 6, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.72
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.72
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10005.png

Downloads & links

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Map

FileDownload / File: emd_10005.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNative bacterioferritin from Mycobacterium smegmatis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.22 Å/pix.
x 64 pix.
= 270.08 Å		4.22 Å/pix.
x 64 pix.
= 270.08 Å		4.22 Å/pix.
x 64 pix.
= 270.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.72 / Movie #1: 3.72
Minimum - Maximum-2.7886474 - 6.3598986
Average (Standard dev.)0.0000000035 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-8-8-8
Dimensions646464
Spacing646464
CellA=B=C: 270.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.224.224.22
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z270.080270.080270.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-8-8-8
NC/NR/NS646464
D min/max/mean-2.7896.3600.000

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Supplemental data

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Sample components

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Entire : Bacterioferritin; ferritin family protein

EntireName: Bacterioferritin; ferritin family protein
Components
  • Complex: Bacterioferritin; ferritin family protein

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Supramolecule #1: Bacterioferritin; ferritin family protein

SupramoleculeName: Bacterioferritin; ferritin family protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Octahedral symmetry imposed
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Location in cell: Cytoplasm
Molecular weightExperimental: 480 KDa

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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
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 selectionDetails: Manual picking
Startup modelType of model: OTHER
Details: Initial model generated in EMAN Common Lines with octahedral symmetry imposed
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Details: Octahedral symmetry imposed / Number images used: 1873
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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