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- EMDB-1530: Structure of hexameric DyP from Brevibacterium linens -

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Basic information

Entry
Database: EMDB / ID: 1530
TitleStructure of hexameric DyP from Brevibacterium linens
Keywordsprotein complex / hexamer / peroxidase / dye-decolorizing peroxidase / heme containing peroxidase
SampleStructure of hexameric DyP from Brevibacterium linens
SourceBrevibacterium linens / bacteria / ブレビバクテリウム・リネンス
Map dataStructure of hexameric DyP from Brevibacterium linens
Methodsingle particle reconstruction, at 16 Å resolution
AuthorsSutter M / Boehringer D / Gutmann S / Gunther S / Prangishvili D / Loessner MJ / Stetter KO / Weber-Ban E / Ban N
CitationNat. Struct. Mol. Biol., 2008, 15, 939-947

Nat. Struct. Mol. Biol., 2008, 15, 939-947 StrPapers
Structural basis of enzyme encapsulation into a bacterial nanocompartment.
Markus Sutter / Daniel Boehringer / Sascha Gutmann / Susanne Günther / David Prangishvili / Martin J Loessner / Karl O Stetter / Eilika Weber-Ban / Nenad Ban

DateDeposition: Jun 24, 2008 / Header (metadata) release: Jun 24, 2008 / Map release: Jun 11, 2009 / Last update: Jun 24, 2008

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.18
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1530.map.gz (map file in CCP4 format, 1025 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
2.8 Å/pix.
= 179.2 Å
64 pix
2.8 Å/pix.
= 179.2 Å
64 pix
2.8 Å/pix.
= 179.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:0.1 (by author), 0.18 (movie #1):
Minimum - Maximum-1.38813 - 0.944775
Average (Standard dev.)-0.00162246 (0.125636)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-31-32
Limit313231
Spacing646464
CellA=B=C: 179.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z179.200179.200179.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS-31-32-32
NC/NR/NS646464
D min/max/mean-1.3880.945-0.002

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Supplemental data

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Sample components

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Entire Structure of hexameric DyP from Brevibacterium linens

EntireName: Structure of hexameric DyP from Brevibacterium linens / Details: monodisperse / Number of components: 1 / Oligomeric State: hexamer
MassTheoretical: 240 kDa

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Component #1: protein, dye-decolorizing peroxidase

ProteinName: dye-decolorizing peroxidase / a.k.a: Dyp / Oligomeric Details: hexamer / Recombinant expression: Yes / Number of Copies: 6
MassTheoretical: 40 kDa
SourceSpecies: Brevibacterium linens / bacteria / ブレビバクテリウム・リネンス
Strain: M18
Source (engineered)Expression System: Escherichia coli rosetta / bacteria / image: Escherichia coli
Vector: pET21a
External referencesInterPro: InterPro: 006314

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Experimental details

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Sample preparation

Specimen stateparticle
Support filmcarbon coated 200 mesh copper grid
Staining2% w/v uranyl acetate
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 100000 X (nominal), 100000 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 700 - 1500 nm / Energy filter: Tridiem Gatan
Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 295 K
CameraDetector: GATAN ULTRASCAN 1000 (2k x 2k)

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Image acquisition

Image acquisitionSampling size: 1.4 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 2878 / Applied symmetry: D3 (2*3 fold dihedral)
3D reconstructionAlgorithm: angular reconstitution / Software: IMAGIC-5 / CTF correction: Each image / Resolution: 16 Å / Resolution method: FSC 3 sigma square root(6)

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