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Yorodumi- PDB-3i27: Structure of bovine torovirus Hemagglutinin-Esterase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i27 | |||||||||
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Title | Structure of bovine torovirus Hemagglutinin-Esterase in complex with receptor | |||||||||
Components | Hemagglutinin-esterase | |||||||||
Keywords | HYDROLASE / SGNH-hydrolase fold / Swiss roll / Envelope protein / Glycoprotein / Hemagglutinin / Membrane / Transmembrane / Virion / Cell membrane | |||||||||
Function / homology | Function and homology information sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase activity / sialate O-acetylesterase / carbohydrate binding / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Breda virus serotype 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Zeng, Q.H. / Huizinga, E.G. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structural basis for ligand and substrate recognition by torovirus hemagglutinin esterases Authors: Langereis, M.A. / Zeng, Q.H. / Gerwig, G.J. / Frey, B. / von Itzstein, M. / Kamerling, J.P. / de Groot, R.J. / Huizinga, E.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i27.cif.gz | 323.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i27.ent.gz | 261.4 KB | Display | PDB format |
PDBx/mmJSON format | 3i27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i27_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 3i27_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 3i27_validation.xml.gz | 61.6 KB | Display | |
Data in CIF | 3i27_validation.cif.gz | 91 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/3i27 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/3i27 | HTTPS FTP |
-Related structure data
Related structure data | 3i1kC 3i1lC 3i26SC 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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2 |
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Unit cell |
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-Components
-Protein / Non-polymers , 2 types, 1016 molecules ABCD
#1: Protein | Mass: 42774.805 Da / Num. of mol.: 4 / Fragment: residues 15-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Breda virus serotype 1 / Strain: Breda virus serotype 1 / Gene: HE / Plasmid: S1-Ig / Cell line (production host): HEK293S cell line / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: P0C0V9, sialate O-acetylesterase #7: Water | ChemComp-HOH / | |
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-Sugars , 5 types, 15 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: 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: Sugar | ChemComp-NAG / #6: Sugar | ChemComp-SID / | |
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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: 3.05 Å3/Da / Density % sol: 59.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M sodium malonate, 0.1M Bis-Tris propane, pH 8.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9732 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9732 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 141526 / Num. obs: 141525 / % possible obs: 99.5 % / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / Num. unique all: 20262 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3I26 Resolution: 2→48.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.202 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.132 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.257 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→48.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.998→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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