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Yorodumi- PDB-6n4d: The crystal structure of neuramindase from A/canine/IL/11613/2015... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n4d | |||||||||
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Title | The crystal structure of neuramindase from A/canine/IL/11613/2015 (H3N2) influenza virus. | |||||||||
Components | Neuraminidase | |||||||||
Keywords | VIRAL PROTEIN / Neuraminidase / canine influenza virus | |||||||||
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 | unidentified influenza virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | |||||||||
Authors | Yang, H. / Stevens, J. | |||||||||
Citation | Journal: J. Infect. Dis. / Year: 2017 Title: Assessment of Molecular, Antigenic, and Pathological Features of Canine Influenza A(H3N2) Viruses That Emerged in the United States. Authors: Pulit-Penaloza, J.A. / Simpson, N. / Yang, H. / Creager, H.M. / Jones, J. / Carney, P. / Belser, J.A. / Yang, G. / Chang, J. / Zeng, H. / Thor, S. / Jang, Y. / Killian, M.L. / Jenkins-Moore, ...Authors: Pulit-Penaloza, J.A. / Simpson, N. / Yang, H. / Creager, H.M. / Jones, J. / Carney, P. / Belser, J.A. / Yang, G. / Chang, J. / Zeng, H. / Thor, S. / Jang, Y. / Killian, M.L. / Jenkins-Moore, M. / Janas-Martindale, A. / Dubovi, E. / Wentworth, D.E. / Stevens, J. / Tumpey, T.M. / Davis, C.T. / Maines, T.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n4d.cif.gz | 598.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n4d.ent.gz | 501.9 KB | Display | PDB format |
PDBx/mmJSON format | 6n4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/6n4d ftp://data.pdbj.org/pub/pdb/validation_reports/n4/6n4d | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43703.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0H3YBU9 |
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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-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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 | ChemComp-NAG / |
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-Non-polymers , 2 types, 286 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: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7 Details: 0.2M Calcium acetate, 0.1M TrispH7.0, 20% (w/v) PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 143267 / % possible obs: 99.9 % / Redundancy: 7.2 % / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.8→1.86 Å |
-Processing
Software |
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Refinement | Resolution: 1.8→49.43 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.262 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.134 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.456 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→49.43 Å
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Refine LS restraints |
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