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- EMDB-12146: Brevibacterium linens encapsulin-associated Dye-decolorizing pero... -

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Basic information

Entry
Database: EMDB / ID: EMD-12146
TitleBrevibacterium linens encapsulin-associated Dye-decolorizing peroxidase
Map dataBrevibacterium linens encapsulin-associated Dye-decolorizing peroxidase
Sample
  • Complex: Dye-decolorizing peroxidase
    • Protein or peptide: Dye-decolorizing peroxidase
Biological speciesBrevibacterium linens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsAllende-Ballestero C / Luque D / Klem R / Cornelissen JJLM / Caston JR
CitationJournal: To Be Published
Title: Three-dimensional cryoEM structure of Brevibacterium linens encapsulin
Authors: Allende-Ballestero C / Luque D / Klem R / Cornelissen JJLM / Caston JR
History
DepositionDec 21, 2020-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12146.png

Downloads & links

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Map

FileDownload / File: emd_12146.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBrevibacterium linens encapsulin-associated Dye-decolorizing peroxidase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 150 pix.
= 157.05 Å		1.05 Å/pix.
x 150 pix.
= 157.05 Å		1.05 Å/pix.
x 150 pix.
= 157.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0036
Minimum - Maximum-0.031715147 - 0.05556074
Average (Standard dev.)0.00041750004 (±0.0027586753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-75-75-75
Dimensions150150150
Spacing150150150
CellA=B=C: 157.05 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Dye-decolorizing peroxidase

EntireName: Dye-decolorizing peroxidase
Components
  • Complex: Dye-decolorizing peroxidase
    • Protein or peptide: Dye-decolorizing peroxidase

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Supramolecule #1: Dye-decolorizing peroxidase

SupramoleculeName: Dye-decolorizing peroxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brevibacterium linens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Dye-decolorizing peroxidase

MacromoleculeName: Dye-decolorizing peroxidase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Brevibacterium linens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALPNGKTPQ HVLGPPAPAA VFLVLTVRSG AEAEAKDFLG DIAGVVRSVG FRAREDHLSC VTGIGAELWD RMFDAPRPAG LHPFIEQRGD VHTAPSTPGD LLFHIRARRM DLCFELARQL VGELGDAVSV VDEVHGFRYF DERDIMGFVD GTENPEDQEA VDSVFTPTGG ...String:
MALPNGKTPQ HVLGPPAPAA VFLVLTVRSG AEAEAKDFLG DIAGVVRSVG FRAREDHLSC VTGIGAELWD RMFDAPRPAG LHPFIEQRGD VHTAPSTPGD LLFHIRARRM DLCFELARQL VGELGDAVSV VDEVHGFRYF DERDIMGFVD GTENPEDQEA VDSVFTPTGG DDPASSTYVI VQKYTHDMAA WEALSVEDQE AAFGRHKLSD MEFPDEDKAP NSHLILNTIE DEDGTEHKIV RDNMVFGSVE SGEFGTYFIG YAADVSVTEQ MLENMFIGNP RGTYDRILDF STAQTGGLFF VPSQDFLDDP DGELAAAEPS DAQNDDPASA SARVEETDPP NPASADDPAP ADDSLGIGSL RRRDQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
20.0 mMTris
150.0 mMAmmonium Chloride
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 38.85 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.2 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 309778
CTF correctionSoftware: (Name: CTFFIND (ver. 4), RELION (ver. 3))
Startup modelType of model: INSILICO MODEL / In silico model: Created with EMAN2
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 30473
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

3qnr


Chain - Chain ID: A
RefinementProtocol: FLEXIBLE FIT

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