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Yorodumi- PDB-6iig: crystal structure of H5N2 hemagglutinin G228S mutant With 6SLN fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iig | |||||||||
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Title | crystal structure of H5N2 hemagglutinin G228S mutant With 6SLN 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 | unidentified influenza virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.208 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 | 6iig.cif.gz | 218.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iig.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 6iig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6iig ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6iig | HTTPS FTP |
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-Related structure data
Related structure data | 5ykcSC 5yt8C 5yt9C 5z88C 6ijtC 6in5C 6kcjC 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: 66360.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus / Production host: unidentified baculovirus / References: UniProt: A0A059VBQ9*PLUS |
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#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.45 % |
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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 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 12660 / % possible obs: 99.99 % / Redundancy: 4.6 % / CC1/2: 0.967 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.062 / Rrim(I) all: 0.133 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.596 / CC1/2: 0.91 / Rpim(I) all: 0.325 / Rrim(I) all: 0.682 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YKC Resolution: 3.208→27.384 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.208→27.384 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: 120.5886 Å / Origin y: -14.944 Å / Origin z: 61.0772 Å
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Refinement TLS group | Selection details: all |