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Yorodumi- PDB-5jif: Crystal structure of mouse hepatitis virus strain DVIM Hemaggluti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jif | |||||||||
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Title | Crystal structure of mouse hepatitis virus strain DVIM Hemagglutinin-Esterase | |||||||||
Components | Hemagglutinin-esterase | |||||||||
Keywords | VIRAL PROTEIN / Hemagglutin / Esterase / Hepatitis virus / Coronavirus | |||||||||
Function / homology | Function and homology information sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / membrane => GO:0016020 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||
Biological species | Murine coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Zeng, Q.H. / Bakkers, M.J.G. / Feitsma, L.J. / de Groot, R.J. / Huizinga, E.G. | |||||||||
Funding support | Netherlands, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation. Authors: Bakkers, M.J. / Zeng, Q. / Feitsma, L.J. / Hulswit, R.J. / Li, Z. / Westerbeke, A. / van Kuppeveld, F.J. / Boons, G.J. / Langereis, M.A. / 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 | 5jif.cif.gz | 315.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jif.ent.gz | 255.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jif_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 5jif_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 5jif_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 5jif_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/5jif ftp://data.pdbj.org/pub/pdb/validation_reports/ji/5jif | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 24 - 386 / Label seq-ID: 3 - 365
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43017.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murine coronavirus / Strain: DVIM / Gene: HE, 2b / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O92367, sialate O-acetylesterase |
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-Sugars , 4 types, 15 molecules
#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: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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 #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 227 molecules
#5: Chemical | #6: Chemical | #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: 2.79 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris-HCl pH 8.0, 0.05M NaF, 16% w/v PEG3350, 10% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.41 Å / Num. obs: 65139 / % possible obs: 99.2 % / Redundancy: 9.24 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 7 % / Rmerge(I) obs: 1.184 / Mean I/σ(I) obs: 2.3 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MHV-S Resolution: 2→39.73 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 9.477 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.151 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.651 Å2
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Refinement step | Cycle: 1 / Resolution: 2→39.73 Å
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Refine LS restraints |
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