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Yorodumi- PDB-7xyc: CryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xyc | ||||||
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Title | CryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 in vitro | ||||||
Components | phage tail fiber | ||||||
Keywords | VIRAL PROTEIN / Phage type II tail fiber | ||||||
Biological species | Klebsiella phage Kp7 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 | 7xyc.cif.gz | 275.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xyc.ent.gz | 225.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xyc_validation.pdf.gz | 731.7 KB | Display | wwPDB validaton report |
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Full document | 7xyc_full_validation.pdf.gz | 751.9 KB | Display | |
Data in XML | 7xyc_validation.xml.gz | 52 KB | Display | |
Data in CIF | 7xyc_validation.cif.gz | 78.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/7xyc ftp://data.pdbj.org/pub/pdb/validation_reports/xy/7xyc | HTTPS FTP |
-Related structure data
Related structure data | 33519MC 7xy1C 7y1cC 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: 61210.270 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella phage Kp7 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta |
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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 Kp7 type II tail fiber / Type: COMPLEX / Details: Trimer of tail fiber proteins / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Klebsiella phage Kp7 (virus) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Rosetta |
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 R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 3710 / Height: 3710 |
-Processing
EM software | Name: RELION / Version: 3.0.8 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING ONLY |
Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113834 / Symmetry type: POINT |
Atomic model building | B value: 146 / Protocol: AB INITIO MODEL / Space: REAL |