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Yorodumi- PDB-5huk: The crystal structure of neuraminidase from A/Northern pintail/Wa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5huk | |||||||||
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Title | The crystal structure of neuraminidase from A/Northern pintail/Washington/40964/2014 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: 2.45 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 | 5huk.cif.gz | 608.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5huk.ent.gz | 510.6 KB | Display | PDB format |
PDBx/mmJSON format | 5huk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/5huk ftp://data.pdbj.org/pub/pdb/validation_reports/hu/5huk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44117.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Northern pintail/Washington/40964/2014(H5N2)) Strain: A/Northern pintail/Washington/40964/2014(H5N2) / Gene: NA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0C4WXC5, exo-alpha-sialidase |
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-Sugars , 3 types, 12 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 2 types, 393 molecules
#4: Chemical | ChemComp-CA / #6: 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: 3.58 Å3/Da / Density % sol: 65.6 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: 0.1M Sodium Citrate: Citric acid, pH 5.5, 40% PEG (v/v) 600 |
-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: Jun 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 91882 / % possible obs: 98.3 % / Redundancy: 6.2 % / Net I/σ(I): 24.9 |
-Processing
Software |
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Refinement | Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.92 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.178 / 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: 46.004 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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