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- PDB-3jb5: Capsid Structure of the Propionibacterium acnes Bacteriophage ATC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jb5 | ||||||
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Title | Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear | ||||||
![]() | major capsid protein | ||||||
![]() | VIRUS / acne / bacteriophage / HK97-like | ||||||
Function / homology | Gp6![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
![]() | Chiou, J. / Zhang, X. / Marinelli, L.J. / Modlin, R.L. / Zhou, Z.H. | ||||||
![]() | ![]() Title: Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear Authors: Chiou, J. / Zhang, X. / Marinelli, L.J. / Modlin, R.L. / Zhou, Z.H. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 342.1 KB | Display | ![]() |
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PDB format | ![]() | 287.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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3 | ![]()
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5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 32765.082 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 |
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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 |
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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: ![]() |
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 |
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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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