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Yorodumi- PDB-5ykc: crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ykc | |||||||||
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Title | crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012 | |||||||||
Components | Hemagglutinin | |||||||||
Keywords | VIRAL PROTEIN / influenza virus / H5N2 | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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 Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.823 Å | |||||||||
Authors | Lin, T.H. / Lee, M.S. / Wu, W.G. | |||||||||
Citation | Journal: To Be Published Title: crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012 Authors: Lin, T.H. / Lee, M.S. / Wu, W.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ykc.cif.gz | 616 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ykc.ent.gz | 509.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ykc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ykc_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 5ykc_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 5ykc_validation.xml.gz | 57 KB | Display | |
Data in CIF | 5ykc_validation.cif.gz | 75.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5ykc ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5ykc | HTTPS FTP |
-Related structure data
Related structure data | 5yt8C 5yt9C 5z88C 6iigC 6ijtC 6in5C 6kcjC 5e2yS 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
#1: Protein | Mass: 66330.594 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/chicken/Taiwan/0502/2012(H5N2)) Strain: A/chicken/Taiwan/0502/2012(H5N2) / Production host: unidentified baculovirus / References: UniProt: A0A059VBQ9*PLUS #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: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KJ720208.1 FOR THIS SEQUENCE. | |
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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: 2.85 Å3/Da / Density % sol: 62.25 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M tris, 0.2M MgCl, 14% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.823→29.04 Å / Num. obs: 46855 / % possible obs: 85.41 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.14 |
Reflection shell | Resolution: 2.82→2.92 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.685 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5e2y Resolution: 2.823→29.036 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.823→29.036 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -30.6151 Å / Origin y: -51.1159 Å / Origin z: 17.8827 Å
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Refinement TLS group | Selection details: all |