+Open data
-Basic information
Entry | Database: PDB / ID: 8rvj | ||||||
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Title | Engineered Encapsulin P3P4 | ||||||
Components | Type 1 encapsulin shell protein | ||||||
Keywords | VIRUS LIKE PARTICLE / Encapsulin / Nanocage / Compartment / Storage / Complex | ||||||
Function / homology | Type 1 encapsulin shell protein / : / Encapsulating protein for peroxidase / encapsulin nanocompartment / iron ion transport / intracellular iron ion homeostasis / Type 1 encapsulin shell protein Function and homology information | ||||||
Biological species | Bacillus thermotolerans (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Satler, T. / Jerala, R. | ||||||
Funding support | Slovenia, 1items
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Citation | Journal: To Be Published Title: Structure of engineered encapsulin P3P4 Authors: Satler, T. / Jerala, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rvj.cif.gz | 267.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rvj.ent.gz | 175.5 KB | Display | PDB format |
PDBx/mmJSON format | 8rvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rvj_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8rvj_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8rvj_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 8rvj_validation.cif.gz | 76.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/8rvj ftp://data.pdbj.org/pub/pdb/validation_reports/rv/8rvj | HTTPS FTP |
-Related structure data
Related structure data | 19521MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 36881.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thermotolerans (bacteria) / Gene: enc, QY95_01592 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F5HPP7 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Engineered Encapsulin P3P4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Bacillus thermotolerans (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software | Name: cryoSPARC / Version: 3.3 / Category: 3D reconstruction | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3082 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.65 Å2 | ||||||||||||||||||||||||
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