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- EMDB-10004: Native encapsulated dye decolourising type peroxidase from Mycoba... -

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Basic information

Entry
Database: EMDB / ID: EMD-10004
TitleNative encapsulated dye decolourising type peroxidase from Mycobacterium smegmatis
Map dataEncapsulated dye decolourising type peroxidase
Sample
  • Complex: Encapsulated DyP type peroxidase
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 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: 11.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 11.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10004.png

Downloads & links

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Map

FileDownload / File: emd_10004.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEncapsulated dye decolourising type peroxidase
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: 11.1 / Movie #1: 11.1
Minimum - Maximum-11.868299 - 27.44111
Average (Standard dev.)-0.0000000451 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-17-17-17
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
MAP C/R/S123
start NC/NR/NS-17-17-17
NC/NR/NS128128128
D min/max/mean-11.86827.441-0.000

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Supplemental data

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Sample components

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Entire : Encapsulated DyP type peroxidase

EntireName: Encapsulated DyP type peroxidase
Components
  • Complex: Encapsulated DyP type peroxidase

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Supramolecule #1: Encapsulated DyP type peroxidase

SupramoleculeName: Encapsulated DyP type peroxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Mask applied to encapsulin shell
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Location in cell: Cytoplasm
Molecular weightExperimental: 222 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 selectionNumber selected: 207 / Details: Manual picking
Startup modelType of model: OTHER
Details: Initial model generated in EMAN Common Lines using encapsulin particles with mask applied. C3 symmetry imposed.
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF
Details: D3 symmetry imposed. 15 angstrom low pass filter used. Mask radius of 70 angstrom.
Number images used: 207
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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