+Open data
-Basic information
Entry | Database: PDB / ID: 1yue | ||||||
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Title | Bacteriophage T4 capsid vertex protein gp24 | ||||||
Components | Head vertex protein Gp24 | ||||||
Keywords | VIRAL PROTEIN / gp24 / bacteriophage T4 / capsid protein / vertex / bacteriophage / virus / HK97 / MAD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Fokine, A. / Leiman, P.G. / Shneider, M.M. / Ahvazi, B. / Boeshans, K.M. / Steven, A.C. / Black, L.W. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry. Authors: Fokine, A. / Leiman, P.G. / Shneider, M.M. / Ahvazi, B. / Boeshans, K.M. / Steven, A.C. / Black, L.W. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yue.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yue.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yue_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 1yue_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 1yue_validation.xml.gz | 18 KB | Display | |
Data in CIF | 1yue_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/1yue ftp://data.pdbj.org/pub/pdb/validation_reports/yu/1yue | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47273.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 24 / Plasmid: pET-23 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P19896 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 0.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES-Na pH 7.5; 10% v/v isopropanol; 0.2 M Sodium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→35 Å / Num. all: 164088 / Num. obs: 11621 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Biso Wilson estimate: 108 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: High values of atomic B factors reflect the disorder of the crystal. The mosaisity was ~1.5 deg
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Solvent computation | Solvent model: Flat Model / Bsol: 48.1183 Å2 / ksol: 0.30571 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→35 Å
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Refine LS restraints |
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