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- PDB-5yt9: Crystal structure of H5 hemagglutinin G228S mutant from A/chicken... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yt9 | ||||||
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Title | Crystal structure of H5 hemagglutinin G228S mutant from A/chicken/Taiwan/0502/2012 | ||||||
![]() | Hemagglutinin | ||||||
![]() | VIRAL PROTEIN / influenza virus / H5N2 | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, T.H. / Lee, M.S. / Wu, W.G. / Liu, J.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012 Authors: Lin, T.H. / Lee, M.S. / Wu, W.G. / Liu, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.7 KB | Display | ![]() |
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PDB format | ![]() | 173.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.7 KB | Display | ![]() |
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Full document | ![]() | 459.6 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ykcSC ![]() 5yt8C ![]() 5z88C ![]() 6iigC ![]() 6ijtC ![]() 6in5C ![]() 6kcjC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 / Mutation: G228S, R327F, K328T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HA / Cell line (production host): sf21 / Production host: ![]() ![]() |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.73 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, 0.2M MgCl, 16% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.766→30 Å / Num. obs: 19702 / % possible obs: 99.71 % / Redundancy: 2.6 % / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.77→2.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.43 / CC1/2: 0.806 / Rpim(I) all: 0.346 / Rrim(I) all: 0.59 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YKC Resolution: 2.766→29.834 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.766→29.834 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: 120.8483 Å / Origin y: -15.0571 Å / Origin z: 61.5686 Å
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Refinement TLS group | Selection details: all |