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Yorodumi- PDB-7w83: Structure of the C-terminal head domain of the fowl adenovirus ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w83 | ||||||
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Title | Structure of the C-terminal head domain of the fowl adenovirus type 4 fiber 2 | ||||||
Components | Fiber-2 protein | ||||||
Keywords | VIRAL PROTEIN / fowl adenovirus type 4 / fiber 2 | ||||||
Function / homology | Fiber protein 1, C-terminal / Fiber protein, C-terminal domain superfamily / C-terminal head domain of the fowl adenovirus type 1 long fibre / Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / virion attachment to host cell / Fiber-2 protein Function and homology information | ||||||
Biological species | Fowl aviadenovirus 4 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Jin, Q.Y. / Zhang, G.P. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of the C-terminal head domain of the fowl adenovirus type 4 fiber 2 Authors: Jin, Q.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w83.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w83.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 7w83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/7w83 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w83 | HTTPS FTP |
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-Related structure data
Related structure data | 2vtwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23765.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fowl aviadenovirus 4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A346SCF3 #2: Water | ChemComp-HOH / | |
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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: 2.13 Å3/Da / Density % sol: 42.24 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.1 M Sodium acetate trihydrate pH 7.0 12% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 273 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→50.48 Å / Num. obs: 98150 / % possible obs: 98.8 % / Redundancy: 17.3 % / CC1/2: 0.998 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.29→1.32 Å / Num. unique obs: 6455 / CC1/2: 0.741 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VTW Resolution: 1.29→50.48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.99 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.48 Å2 / Biso mean: 16.56 Å2 / Biso min: 7.53 Å2
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Refinement step | Cycle: final / Resolution: 1.29→50.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.29→1.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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