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Yorodumi- PDB-6kcj: Crystal structure of H5N2 hemagglutinin Apo-Q226L mutant from A/c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kcj | ||||||
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Title | Crystal structure of H5N2 hemagglutinin Apo-Q226L mutant 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: 2.46 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 | 6kcj.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kcj.ent.gz | 175.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kcj_validation.pdf.gz | 747.1 KB | Display | wwPDB validaton report |
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Full document | 6kcj_full_validation.pdf.gz | 758.3 KB | Display | |
Data in XML | 6kcj_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 6kcj_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kcj ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kcj | HTTPS FTP |
-Related structure data
Related structure data | 5ykcSC 5yt8C 5yt9C 5z88C 6iigC 6ijtC 6in5C 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: 66315.625 Da / Num. of mol.: 1 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) / Gene: HA / Production host: unidentified baculovirus / References: UniProt: A0A059VBQ9 |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 55.75 % |
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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 / 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: 2.46→30 Å / Num. obs: 27258 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.042 / Rrim(I) all: 0.14 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.46→2.55 Å / Rmerge(I) obs: 1.415 / Mean I/σ(I) obs: 2 / Num. unique obs: 2682 / CC1/2: 0.83 / Rpim(I) all: 0.441 / Rrim(I) all: 1.483 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YKC Resolution: 2.46→28.152 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→28.152 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: 119.7962 Å / Origin y: -14.8325 Å / Origin z: 60.9848 Å
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Refinement TLS group | Selection details: all |