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Yorodumi- PDB-6hg0: Influenza A Virus N9 Neuraminidase complex with NANA (Tern/Australia). -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hg0 | |||||||||
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Title | Influenza A Virus N9 Neuraminidase complex with NANA (Tern/Australia). | |||||||||
Components | Neuraminidase | |||||||||
Keywords | HYDROLASE / Complex / NANA / N-Acetylneuraminic acid / Neuraminidase / N9 / Influenza / Virus / Enzyme / Inhibitor / Tern | |||||||||
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 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Salinger, M.T. / Hobbs, J.R. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Garman, E.F. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (In preparation) Authors: Salinger, M.T. / Hobbs, J.R. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Garman, E.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hg0.cif.gz | 226.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hg0.ent.gz | 179.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/6hg0 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/6hg0 | HTTPS FTP |
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-Related structure data
Related structure data | 6hcxC 6hfcC 6hfyC 6hgbC 7nn9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9) References: UniProt: P03472, exo-alpha-sialidase |
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-Sugars , 3 types, 5 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 | ||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | |
-Non-polymers , 5 types, 735 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PO4 / | #8: Chemical | ChemComp-K / | #9: 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: 2.83 Å3/Da / Density % sol: 56.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: N9 crystals were grown by hanging-drop vapour diffusion against a reservoir of 1.9M potassium phosphate, pH 6.8, starting with equal volumes of N9 NA (10-15 mg/ml in water) and potassium ...Details: N9 crystals were grown by hanging-drop vapour diffusion against a reservoir of 1.9M potassium phosphate, pH 6.8, starting with equal volumes of N9 NA (10-15 mg/ml in water) and potassium phosphate buffer 1.4M KH2PO4:3M K2HPO4 in ratio 8:4, pH 6.6 at 20 degrees celsius. Inhibitor complexes obtained by soaking N9 crystals in a solution of 1.4M potassium phosphate buffer, pH 6.8, containing 5mM of inhibitor for 3 hours at 4 degrees celsius. Soaked in glycerol cryo-buffer. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→48.47 Å / Num. obs: 122385 / % possible obs: 99.7 % / Redundancy: 14 % / Rsym value: 0.097 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 6028 / Rsym value: 0.335 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NN9 Resolution: 1.3→48.47 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.974 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.031 / 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: 13.497 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→48.47 Å
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Refine LS restraints |
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