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Yorodumi- PDB-5z88: Crystal structure of H5 hemagglutinin G228S mutant with 3SLN from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z88 | |||||||||
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Title | Crystal structure of H5 hemagglutinin G228S mutant with 3SLN from A/chicken/Taiwan/0502/2012 | |||||||||
Components | Hemagglutinin | |||||||||
Keywords | VIRAL PROTEIN / influenza virus / H5N2 | |||||||||
Function / homology | Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Alpha-Beta Complex / Alpha Beta Function and homology information | |||||||||
Biological species | unidentified influenza virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Lin, T.H. / Lee, M.S. / Wu, W.G. / 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 | 5z88.cif.gz | 218.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z88.ent.gz | 172 KB | Display | PDB format |
PDBx/mmJSON format | 5z88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/5z88 ftp://data.pdbj.org/pub/pdb/validation_reports/z8/5z88 | HTTPS FTP |
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-Related structure data
Related structure data | 5ykcC 5yt8C 5yt9SC 6iigC 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: Baculoviridae (virus) |
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#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-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: 2.77 Å3/Da / Density % sol: 55.56 % |
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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: Aug 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→30 Å / Num. obs: 13555 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.966 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.506 / CC1/2: 0.87 / Rpim(I) all: 0.324 / Rrim(I) all: 0.605 / Rsym value: 0.301 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YT9 Resolution: 3→28.121 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→28.121 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: 119.5715 Å / Origin y: -14.8024 Å / Origin z: 60.8909 Å
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Refinement TLS group | Selection details: all |