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Yorodumi- PDB-3jb5: Capsid Structure of the Propionibacterium acnes Bacteriophage ATC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jb5 | ||||||
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Title | Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear | ||||||
Components | major capsid protein | ||||||
Keywords | VIRUS / acne / bacteriophage / HK97-like | ||||||
Function / homology | Gp6 Function and homology information | ||||||
Biological species | Propionibacterium phage PA6 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Chiou, J. / Zhang, X. / Marinelli, L.J. / Modlin, R.L. / Zhou, Z.H. | ||||||
Citation | Journal: To be Published Title: Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear Authors: Chiou, J. / Zhang, X. / Marinelli, L.J. / Modlin, R.L. / Zhou, Z.H. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jb5.cif.gz | 342.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jb5.ent.gz | 287.6 KB | Display | PDB format |
PDBx/mmJSON format | 3jb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jb5 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jb5 | HTTPS FTP |
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-Related structure data
Related structure data | 6398MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 32765.082 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Propionibacterium phage PA6 (virus) / References: UniProt: A4K473 |
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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: Propionibacterium acnes bacteriophage ATCC_Clear / Type: VIRUS |
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Molecular weight | Value: 33 MDa / Experimental value: YES |
Details of virus | Empty: NO / Enveloped: NO / Host category: BACTERIA(EUBACTERIA) / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Propionibacterium acnes / Strain: 6919 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Purified sample was applied to a Quantifoil grid. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % Details: Blot for 15 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Method: Blot for 15 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: May 16, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 38462 X / Calibrated magnification: 38462 X / Nominal defocus max: 2270 nm / Nominal defocus min: 800 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
Image scans | Num. digital images: 3168 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: FREALIGN / Category: 3D reconstruction | ||||||||||||
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Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27504 / Nominal pixel size: 1.3 Å / Actual pixel size: 1.3 Å Details: (Single particle details: The particles were selected using an in-house selection procedure.) (Single particle--Applied symmetry: I) Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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