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- EMDB-12146: Brevibacterium linens encapsulin-associated Dye-decolorizing pero... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Brevibacterium linens encapsulin-associated Dye-decolorizing peroxidase | |||||||||
![]() | Brevibacterium linens encapsulin-associated Dye-decolorizing peroxidase | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
![]() | Allende-Ballestero C / Luque D / Klem R / Cornelissen JJLM / Caston JR | |||||||||
![]() | ![]() Title: Three-dimensional cryoEM structure of Brevibacterium linens encapsulin Authors: Allende-Ballestero C / Luque D / Klem R / Cornelissen JJLM / Caston JR | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.6 KB 12.6 KB | Display Display | ![]() |
Images | ![]() | 223.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 346 KB | Display | ![]() |
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Full document | ![]() | 345.6 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Brevibacterium linens encapsulin-associated Dye-decolorizing peroxidase | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.047 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Dye-decolorizing peroxidase
Entire | Name: Dye-decolorizing peroxidase |
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Components |
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-Supramolecule #1: Dye-decolorizing peroxidase
Supramolecule | Name: Dye-decolorizing peroxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 240 KDa |
-Macromolecule #1: Dye-decolorizing peroxidase
Macromolecule | Name: Dye-decolorizing peroxidase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 38.85 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated 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 stage | Specimen 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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Refinement | Protocol: FLEXIBLE FIT |