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Yorodumi- PDB-6hgb: Influenza A virus N6 neuraminidase native structure (Duck/England/56). -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hgb | |||||||||
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Title | Influenza A virus N6 neuraminidase native structure (Duck/England/56). | |||||||||
Components | Neuraminidase | |||||||||
Keywords | HYDROLASE / Influenza / A / Native / N6 / Neuraminidase / Duck / Virus / Enzyme / Complex / England / Wild type | |||||||||
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: 1.5 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 | 6hgb.cif.gz | 382.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hgb.ent.gz | 312.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/6hgb ftp://data.pdbj.org/pub/pdb/validation_reports/hg/6hgb | HTTPS FTP |
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-Related structure data
Related structure data | 6hcxC 6hfcC 6hfyC 6hg0C 1v0zS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43011.531 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Influenza A virus (strain A/Duck/England/1/1956 H11N6) Strain: A/Duck/England/1/1956 H11N6 / References: UniProt: Q6XV27, exo-alpha-sialidase |
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-Sugars , 5 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)]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 #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Sugar | |
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-Non-polymers , 5 types, 1638 molecules
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CA / #8: Chemical | #9: Chemical | ChemComp-PEG / #11: 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: 2.43 Å3/Da / Density % sol: 49.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: N6 crystals were grown by hanging-drop vapour diffusion against 1:1 20%(w/v) PEG-3350 and 2 microM CaCl2 in 150mM NaCl at 20 degrees celsius, starting with equal volumes of N6 (20mg/ml in ...Details: N6 crystals were grown by hanging-drop vapour diffusion against 1:1 20%(w/v) PEG-3350 and 2 microM CaCl2 in 150mM NaCl at 20 degrees celsius, starting with equal volumes of N6 (20mg/ml in saline) and 20% (w/v) PEG 3350 and 2 microM in 1% saline. Microseeding with crystals of native N6 was carried out using a super saturated solution of N6 NA in 20% PEG 3350. Temp details: Kept constant throughout. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.93 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30.68 Å / Num. obs: 241948 / % possible obs: 92.1 % / Redundancy: 3.7 % / Rsym value: 0.085 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.5→1.52 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 10672 / Rsym value: 0.184 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V0Z Resolution: 1.5→30.68 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.556 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / 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: 13.965 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→30.68 Å
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