+Open data
-Basic information
Entry | Database: PDB / ID: 7phm | ||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis encapsulin | ||||||
Components | 29 kDa antigen CFP29 | ||||||
Keywords | STRUCTURAL PROTEIN / Encapsulin / icosahedral / oxidative stress response | ||||||
Function / homology | Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / extracellular region / plasma membrane / Type 1 encapsulin shell protein Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||
Authors | Woodward, J.D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Mycobacterium tuberculosis encapsulin Authors: Woodward, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7phm.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7phm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7phm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/7phm ftp://data.pdbj.org/pub/pdb/validation_reports/ph/7phm | HTTPS FTP |
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-Related structure data
Related structure data | 13420MC 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: 29554.072 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: cfp29, Rv0798c / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus / References: UniProt: I6WZG6 |
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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: Empty encapsulin nanocompartment / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 1.73 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET-28a(+) | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 Details: Eluted in: 50mM Tris-HCl, 350mM NaCl, 10mM Imidazol, 10% v/v glycerol at pH 7.4 and diluted 1:2 in distilled water. | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: C-flat 2/2 holey carbon film supported by a standard copper TEM grid and coated with an ultrathin (2-3 nm) continuous carbon film. | |||||||||||||||||||||||||
Specimen support | Details: Glow-discharged using an EMS100X in air: 25 mA at 20 Pa for 30 seconds. Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14133 Details: Data collected in super-resolution mode at 0.53 A/pixel and down-sampled during motion correction to 1.06 A/pixel. |
Image scans | Width: 11520 / Height: 8184 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2000000 Details: 2D class averages were produced using Relion from 1000 manually-picked particles. These were then used as picking templates. | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient Details: Model was generated ab initio using Buccaneer within the CCPEM package and manually corrected using Coot before being refined using Isolde within ChimeraX and Phenix Real Space Refinement ...Details: Model was generated ab initio using Buccaneer within the CCPEM package and manually corrected using Coot before being refined using Isolde within ChimeraX and Phenix Real Space Refinement within the CCPEM package. |