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- PDB-7bcv: Brevibacterium linens encapsulin structure -

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Basic information

Entry
Database: PDB / ID: 7bcv
TitleBrevibacterium linens encapsulin structure
ComponentsLinocin-M18
KeywordsSTRUCTURAL PROTEIN / Bacterial protein compartment
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Type 1 encapsulin shell protein
Function and homology information
Biological speciesBrevibacterium linens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsAllende-Ballestero, C. / Luque, D. / Klem, R. / Cornelissen, J.J.L.M. / Caston, J.R.
CitationJournal: To Be Published
Title: Three-dimensional cryoEM structure of Brevibacterium linens encapsulin
Authors: Allende-Ballestero, C. / Luque, D. / Klem, R. / Cornelissen, J.J.L.M. / Caston, J.R.
History
DepositionDec 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Linocin-M18


Theoretical massNumber of molelcules
Total (without water)28,5911
Polymers28,5911
Non-polymers00
Water00
1
A: Linocin-M18
x 60


Theoretical massNumber of molelcules
Total (without water)1,715,44260
Polymers1,715,44260
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Linocin-M18 / Encapsulin


Mass: 28590.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium linens (bacteria) / Gene: lin / Production host: Escherichia coli (E. coli)
References: UniProt: Q45296, Hydrolases; Acting on peptide bonds (peptidases)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Encapsulin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)Organism: Brevibacterium linens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMTris1
2150 mMAmmonium Chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 38.85 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Xmippparticle selection
2EPUimage acquisition
4CTFFIND4CTF correction
5RELION3CTF correction
11RELION3initial Euler assignment
12RELION3final Euler assignment
13RELION3classification
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 309778
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233829 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT

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