+Open data
-Basic information
Entry | Database: PDB / ID: 6d3b | |||||||||
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Title | INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) APO FORM | |||||||||
Components | Neuraminidase | |||||||||
Keywords | viral protein / hydrolase / NEURAMINIDASE / SIALIDASE / HYDROLASE(O-GLUCOSYL) | |||||||||
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: 1.4 Å | |||||||||
Authors | Streltsov, V.A. / Schmidt, P. / McKimm-Breschkin, J. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: Structure of an Influenza A virus N9 neuraminidase with a tetrabrachion-domain stalk. Authors: Streltsov, V.A. / Schmidt, P.M. / McKimm-Breschkin, J.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d3b.cif.gz | 117.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d3b.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 6d3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/6d3b ftp://data.pdbj.org/pub/pdb/validation_reports/d3/6d3b | HTTPS FTP |
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-Related structure data
Related structure data | 6crdC 6mcxC 7nn9S C: citing same article (ref.) S: Starting model for refinement |
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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: 43836.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The N9 NA from the A/NWS/Tern/Australia/G70C/75 influenza virus was purified as from chicken egg-grown virus Source: (natural) Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9) Strain: A/Tern/Australia/G70C/1975 H11N9 / References: UniProt: P03472, exo-alpha-sialidase |
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-Sugars , 3 types, 3 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-(1-3)-[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 |
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#3: 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 |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 728 molecules
#5: Chemical | #6: Chemical | ChemComp-GOL / #7: 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: 56.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.4 M KH2PO4 + 3.0 M K2HPO4 (2:1) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2011 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→33.07 Å / Num. obs: 92499 / % possible obs: 99 % / Redundancy: 26 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 1.79 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NN9 Resolution: 1.4→33.07 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.891 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.523 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→33.07 Å
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Refine LS restraints |
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