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Yorodumi- PDB-4xjq: The catalytic mechanism of human parainfluenza virus type 3 haema... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xjq | |||||||||
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Title | The catalytic mechanism of human parainfluenza virus type 3 haemagglutinin-neuraminidase revealed | |||||||||
Components | Hemagglutinin-neuraminidase | |||||||||
Keywords | HYDROLASE / Human Parainfluenza Virus 3 Haemagglutinin-Neuraminidase / viral envelope protein | |||||||||
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 / metabolic process / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane ...exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / metabolic process / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human parainfluenza virus 3 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Dirr, L. / El-Deeb, I. / Guillon, P. / Carroux, C. / Chavas, L. / von Itzstein, M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: The catalytic mechanism of human parainfluenza virus type 3 haemagglutinin-neuraminidase revealed. Authors: Dirr, L. / El-Deeb, I.M. / Guillon, P. / Carroux, C.J. / Chavas, L.M. / von Itzstein, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xjq.cif.gz | 203.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xjq.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/4xjq ftp://data.pdbj.org/pub/pdb/validation_reports/xj/4xjq | HTTPS FTP |
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-Related structure data
Related structure data | 4xjrC 1v3eS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50903.637 Da / Num. of mol.: 2 / Fragment: UNP residues 125-572 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parainfluenza virus 3 / Plasmid: pFastbac/CT-TOPO / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G8G134, exo-alpha-sialidase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 |
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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 |
#5: Sugar |
-Non-polymers , 5 types, 652 molecules
#4: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: citrate buffer, ammonium sulphate, PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 24, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 61796 / % possible obs: 93.1 % / Redundancy: 6.7 % / Net I/σ(I): 17.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1V3E Resolution: 1.9→19.78 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.341 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.148 / 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 max: 67.89 Å2 / Biso mean: 23.317 Å2 / Biso min: 10.12 Å2
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Refinement step | Cycle: final / Resolution: 1.9→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.945 Å / Total num. of bins used: 20
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