+Open data
-Basic information
Entry | Database: PDB / ID: 3cl4 | |||||||||
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Title | Crystal structure of bovine coronavirus hemagglutinin-esterase | |||||||||
Components | Hemagglutinin-esterase | |||||||||
Keywords | HYDROLASE / SGNH-hydrolase fold / Swiss roll / Envelope protein / Glycoprotein / Hemagglutinin / Membrane / Transmembrane / Virion | |||||||||
Function / homology | Function and homology information negative regulation of immune system process / sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase activity / sialate O-acetylesterase / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / signaling receptor binding / viral envelope ...negative regulation of immune system process / sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase activity / sialate O-acetylesterase / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / signaling receptor binding / viral envelope / host cell plasma membrane / virion membrane / protein homodimerization activity / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Bovine coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Zeng, Q.H. / Langereis, M.A. / van Vliet, A.L.W. / Huizinga, E.G. / de Groot, R.J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution. Authors: Zeng, Q. / Langereis, M.A. / van Vliet, A.L. / Huizinga, E.G. / de Groot, R.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cl4.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cl4.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cl4_validation.pdf.gz | 833.4 KB | Display | wwPDB validaton report |
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Full document | 3cl4_full_validation.pdf.gz | 837.4 KB | Display | |
Data in XML | 3cl4_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 3cl4_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/3cl4 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/3cl4 | HTTPS FTP |
-Related structure data
Related structure data | 3cl5C 1flcS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 42646.230 Da / Num. of mol.: 1 / Fragment: residues 19-388 Source method: isolated from a genetically manipulated source Details: HEK293S cell line / Source: (gene. exp.) Bovine coronavirus / Strain: Mebus / Gene: HE / Plasmid: S1-Ig / Production host: Homo Sapiens (human) / References: UniProt: P15776, sialate O-acetylesterase | ||||
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#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: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M KH2PO4, 10% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2006 |
Radiation | Monochromator: three diamond monochromators / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→52 Å / Num. all: 39252 / Num. obs: 39252 / % possible obs: 99.6 % / Observed criterion σ(I): -3.7 / Redundancy: 8.4 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5637 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLC chain A resi 40-400 Resolution: 2.1→29.05 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.338 / SU ML: 0.09 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: Engh & Huber / 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: 27.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.094→2.148 Å / Total num. of bins used: 20
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