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Yorodumi- PDB-3cye: Cyrstal structure of the native 1918 H1N1 neuraminidase from a cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cye | |||||||||
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Title | Cyrstal structure of the native 1918 H1N1 neuraminidase from a crystal with lattice-translocation defects | |||||||||
Components | Neuraminidase | |||||||||
Keywords | HYDROLASE / 6-BLADED BETA-PROPELLER / GLYCOPROTEIN / GLYCOSIDASE / MEMBRANE / METAL-BINDING / SIGNAL-ANCHOR / TRANSMEMBRANE / VIRION / lattice-translocation | |||||||||
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 / molecular replacement / Resolution: 1.65 Å | |||||||||
Authors | Zhu, X. / Xu, X. / Wilson, I.A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure determination of the 1918 H1N1 neuraminidase from a crystal with lattice-translocation defects Authors: Zhu, X. / Xu, X. / Wilson, I.A. #1: Journal: To be Published Title: Structural characterization of the 1918 influenza H1N1 neuraminidase Authors: Xu, X. / Zhu, X. / Stevens, J. / Rudd, P.M. / Dwek, R.A. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cye.cif.gz | 335.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cye.ent.gz | 274.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cye_validation.pdf.gz | 678.2 KB | Display | wwPDB validaton report |
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Full document | 3cye_full_validation.pdf.gz | 760.4 KB | Display | |
Data in XML | 3cye_validation.xml.gz | 77.2 KB | Display | |
Data in CIF | 3cye_validation.cif.gz | 110.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/3cye ftp://data.pdbj.org/pub/pdb/validation_reports/cy/3cye | HTTPS FTP |
-Related structure data
Related structure data | 2htyS S: Starting model for refinement |
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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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Number of models | 2 | |||||||||||||||||||||
Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42490.316 Da / Num. of mol.: 2 / Fragment: Ectodomain of neuraminidase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/BREVIG MISSION/1/1918 / Gene: NA / Plasmid: PACGP67 / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HIGH-FIVE BTI-TN-5B1-4 / References: UniProt: Q9IGQ6, exo-alpha-sialidase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-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: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 775 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-GOL / #8: 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: 56.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.16 M CALCIUM ACETATE; 0.08 M CACODYLATE; 14.4% PEG8000; 20% GLYCEROL, PH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.00797 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00797 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 113144 / % possible obs: 97.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.093 / Χ2: 1.966 / Net I/σ(I): 22.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HTY Resolution: 1.65→44.86 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 14.726 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→44.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.687 Å / Total num. of bins used: 20
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