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Yorodumi- PDB-5hun: The crystal structure of neuraminidase from A/gyrfalcon/Washingto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hun | ||||||
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Title | The crystal structure of neuraminidase from A/gyrfalcon/Washington/41088-6/2014 influenza virus | ||||||
Components | Neuraminidase | ||||||
Keywords | VIRAL PROTEIN / neuraminidase / influenza virus / H5Nx | ||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Yang, H. / Carney, P.J. / Guo, Z. / Chang, J.C. / Stevens, J. | ||||||
Citation | Journal: J.Virol. / Year: 2016 Title: Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses. Authors: Yang, H. / Carney, P.J. / Mishin, V.P. / Guo, Z. / Chang, J.C. / Wentworth, D.E. / Gubareva, L.V. / Stevens, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hun.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hun.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/5hun ftp://data.pdbj.org/pub/pdb/validation_reports/hu/5hun | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43960.281 Da / Num. of mol.: 1 / Fragment: unp residues 80-470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/gyrfalcon/Washington/41088-6/2014(H5N8)) Strain: A/gyrfalcon/Washington/41088-6/2014(H5N8) / Gene: NA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0C4WVM3, exo-alpha-sialidase |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: 0.16 M Calcium Acetate, 0.08 M Sodium Cacodylate:HCl pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 19878 / % possible obs: 99.8 % / Redundancy: 6.3 % / Net I/σ(I): 47.8 |
-Processing
Software |
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Refinement | Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.114 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 38.382 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→50 Å
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Refine LS restraints |
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