+Open data
-Basic information
Entry | Database: PDB / ID: 9in6 | ||||||||||||
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Title | Capsid of Vibrio cholerae phage mature VP1 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / phage / virus / vibrio cholera phage | ||||||||||||
Biological species | Vibrio cholerae (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
Authors | Liu, H.R. / Pang, H. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: to be published Title: Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states Authors: Liu, H.R. / Pang, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9in6.cif.gz | 476.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9in6.ent.gz | 400.8 KB | Display | PDB format |
PDBx/mmJSON format | 9in6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9in6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9in6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9in6_validation.xml.gz | 78.7 KB | Display | |
Data in CIF | 9in6_validation.cif.gz | 120.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/9in6 ftp://data.pdbj.org/pub/pdb/validation_reports/in/9in6 | HTTPS FTP |
-Related structure data
Related structure data | 60702MC 8zkkC 8zkmC M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 43886.555 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria) #2: Protein | | Mass: 11801.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria) |
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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: Vibrio cholerae phage / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Vibrio cholerae phage (bacteria) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm |
Image recording | Electron dose: 32 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 441860 / Symmetry type: POINT |