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Yorodumi- PDB-7y1c: CryoEM structure of Klebsiella phage Kp9 tail complex applied wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y1c | ||||||
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Title | CryoEM structure of Klebsiella phage Kp9 tail complex applied with C6 symmetry | ||||||
Components |
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Keywords | VIRUS / Complex / Podophage / short non-contractile tail | ||||||
Biological species | Klebsiella phage Kp9 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å | ||||||
Authors | Huang, L. / Xiang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure and assembly of the Klebsiella pneumoniae phage tail fibers Authors: Huang, L. / Xiang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y1c.cif.gz | 481.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y1c.ent.gz | 381.3 KB | Display | PDB format |
PDBx/mmJSON format | 7y1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y1c_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7y1c_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7y1c_validation.xml.gz | 103.3 KB | Display | |
Data in CIF | 7y1c_validation.cif.gz | 155.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/7y1c ftp://data.pdbj.org/pub/pdb/validation_reports/y1/7y1c | HTTPS FTP |
-Related structure data
Related structure data | 33560MC 7xy1C 7xycC 7y22C 7y23C 7y3tC 7y5sC 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: 58661.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp9 (virus) #2: Protein | Mass: 21374.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp9 (virus) #3: Protein | | Mass: 89081.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp9 (virus) #4: Protein | Mass: 84120.445 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage Kp9 (virus) |
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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: Klebsiella phage Kp9 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Klebsiella phage Kp9 (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Klebsiella pneumoniae ATCC 43816 |
Virus shell | Diameter: 600 nm / Triangulation number (T number): 7 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
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 magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software | Name: RELION / Version: 3.0.8 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C6 (6 fold cyclic) |
3D reconstruction | Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41926 / Symmetry type: POINT |
Atomic model building | B value: 63 / Protocol: AB INITIO MODEL / Space: REAL |