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Yorodumi- PDB-6ijt: Crystal structure of H5N2 hemagglutinin G228S Q226L mutant with 6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ijt | ||||||
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Title | Crystal structure of H5N2 hemagglutinin G228S Q226L 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: 2.9 Å | ||||||
Authors | Lin, T.H. / Lee, M.S. / Liu, J.S. | ||||||
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. / Liu, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ijt.cif.gz | 214.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ijt.ent.gz | 169.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ijt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ijt_validation.pdf.gz | 829.5 KB | Display | wwPDB validaton report |
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Full document | 6ijt_full_validation.pdf.gz | 841.6 KB | Display | |
Data in XML | 6ijt_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6ijt_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/6ijt ftp://data.pdbj.org/pub/pdb/validation_reports/ij/6ijt | HTTPS FTP |
-Related structure data
Related structure data | 5ykcSC 5yt8C 5yt9C 5z88C 6iigC 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: 66345.648 Da / Num. of mol.: 1 / Mutation: G228S, Q226L Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A059VBQ9*PLUS |
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#2: Sugar | ChemComp-SIA / |
Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KJ720208.1 FOR THIS SEQUENCE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.68 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, 0.2M MgCl, 18%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: Nov 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: 2.65→30 Å / Num. obs: 21438 / % possible obs: 99.2 % / Redundancy: 4.6 % / CC1/2: 0.84 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.061 / Rrim(I) all: 0.132 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 2.3 / Rpim(I) all: 1.278 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YKC Resolution: 2.9→28.131 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→28.131 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: 119.7149 Å / Origin y: -14.7872 Å / Origin z: 61.1359 Å
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Refinement TLS group | Selection details: all |