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Yorodumi- PDB-4uo2: Structure of the A_Equine_Richmond_07 H3 haemagglutinin in comple... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4uo2 | |||||||||
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| Title | Structure of the A_Equine_Richmond_07 H3 haemagglutinin in complex with Sialyl Lewis X | |||||||||
Components | (H3 HAEMAGGLUTININ ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / EQUINE / CANINE | |||||||||
| Function / homology | Function and homology informationviral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Vachieri, S.G. / Collins, P.J. / Haire, L.F. / Ogrodowicz, R.W. / Martin, S.R. / Walker, P.A. / Xiong, X. / Gamblin, S.J. / Skehel, J.J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014Title: Recent Evolution of Equine Influenza and the Origin of Canine Influenza. Authors: Collins, P.J. / Vachieri, S.G. / Haire, L.F. / Ogrodowicz, R.W. / Martin, S.R. / Walker, P.A. / Xiong, X. / Gamblin, S.J. / Skehel, J.J. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4uo2.cif.gz | 642.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4uo2.ent.gz | 539.9 KB | Display | PDB format |
| PDBx/mmJSON format | 4uo2.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4uo2_validation.pdf.gz | 6.7 MB | Display | wwPDB validaton report |
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| Full document | 4uo2_full_validation.pdf.gz | 6.7 MB | Display | |
| Data in XML | 4uo2_validation.xml.gz | 57.1 KB | Display | |
| Data in CIF | 4uo2_validation.cif.gz | 78.7 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uo2 ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uo2 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4unwC ![]() 4unxC ![]() 4unyC ![]() 4unzC ![]() 4uo0SC ![]() 4uo1C ![]() 4uo3C ![]() 4uo4C ![]() 4uo5C ![]() 4uo6C ![]() 4uo7C ![]() 4uo8C ![]() 4uo9C ![]() 4uoaC C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
-H3 HAEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF
| #1: Protein | Mass: 36640.312 Da / Num. of mol.: 3 / Fragment: RESIDUES 18-346 Source method: isolated from a genetically manipulated source Description: ANIMAL HEALTH TRUST, NEWMARKET, UNITED KINGDOM / Plasmid: PACGP67 DERIVATIVE / Production host: ![]() #2: Protein | Mass: 19957.035 Da / Num. of mol.: 3 / Fragment: RESIDUES 347-518 Source method: isolated from a genetically manipulated source Description: ANIMAL HEALTH TRUST, NEWMARKET, UNITED KINGDOM / Plasmid: PACGP67 DERIVATIVE / Production host: ![]() |
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-Sugars , 9 types, 26 molecules 
| #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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: Polysaccharide | #8: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: 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 #10: Polysaccharide | Source method: isolated from a genetically manipulated source #11: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 199 molecules 
| #12: Water | ChemComp-HOH / |
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-Details
| Has protein modification | Y |
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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: 2.96 Å3/Da / Density % sol: 58.54 % / Description: NONE |
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-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
| Reflection | Resolution: 2.7→48.46 Å / Num. obs: 55175 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8 |
| Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.38 / % possible all: 99.9 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 4UO0 Resolution: 2.7→107.81 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.898 / SU B: 31.295 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 2.491 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WITH TLS ADDED
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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: 59.141 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.7→107.81 Å
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