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Open data
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Basic information
Entry | Database: PDB / ID: 8rk3 | |||||||||
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Title | Bacteriophage JBD30 baseplate - composite structure | |||||||||
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![]() | VIRUS / bacteriophage JBD30 / virion / baseplate | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.46 Å | |||||||||
![]() | Valentova, L. / Fuzik, T. / Plevka, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and replication of Pseudomonas aeruginosa phage JBD30 Authors: Valentova, L. / Plevka, P. / Fuzik, T. / Novacek, J. / Pospisil, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 19256 ![]() 19257 ![]() 19258 ![]() 19259 ![]() 19260 ![]() 19261 ![]() 19262 ![]() 19263 ![]() 19264 ![]() 19265 ![]() 19266 ![]() 19267 ![]() 19268 ![]() 19269 ![]() 19270 ![]() 19271 ![]() 19272 ![]() 19273 ![]() 19274 ![]() 19280 ![]() 19281 ![]() 19285 ![]() 19439 ![]() 19561 ![]() 8rk4C ![]() 8rk5C ![]() 8rk6C ![]() 8rk7C ![]() 8rk8C ![]() 8rk9C ![]() 8rkaC ![]() 8rkbC ![]() 8rkcC ![]() 8rknC ![]() 8rkoC ![]() 8rkxC ![]() 8rqeC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 18 molecules ABCgOPaWeIEMJFNobd
#1: Protein | Mass: 120920.586 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 29979.053 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 40578.426 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 79898.781 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Virion structural ... , 4 types, 27 molecules UrDcikKQTLRVSYmnGXpHZqsfjhl
#3: Protein | Mass: 62163.148 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 35014.137 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 33358.809 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 26983.729 Da / Num. of mol.: 6 / 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: Pseudomonas phage JBD30 / Type: VIRUS / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 1.713 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Pseudomonas aeruginosa / Strain: BAA-28 | ||||||||||||||||||||
Virus shell | Name: JBD30 capsid / Diameter: 640 nm / Triangulation number (T number): 7 | ||||||||||||||||||||
Buffer solution | pH: 8 / Details: 10 mM NaCl, 10 mM MgSO4, 50 mM Tris-HCl | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: phage titer 10^11 PFU/ml | ||||||||||||||||||||
Specimen support | Details: Gatan Solaris II / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: blotting time 2, blotting force 0, waiting time 5 |
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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 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12356 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
Image scans | Width: 5760 / Height: 4092 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8376 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1780 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |