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Yorodumi- PDB-6v49: The crystal structure of hemagglutinin from A/wedge-tailed shearw... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v49 | |||||||||
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Title | The crystal structure of hemagglutinin from A/wedge-tailed shearwater/Western Australia/2576/1979 (H15N9) | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza / avian / H15 | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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: 2.5 Å | |||||||||
Authors | Yang, H. / Stevens, J. | |||||||||
Citation | Journal: Heliyon / Year: 2020 Title: Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins Authors: Yang, H. / Carney, P.J. / Chang, J. / Stevens, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v49.cif.gz | 595.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v49.ent.gz | 493.5 KB | Display | PDB format |
PDBx/mmJSON format | 6v49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v49_validation.pdf.gz | 475.2 KB | Display | wwPDB validaton report |
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Full document | 6v49_full_validation.pdf.gz | 481.2 KB | Display | |
Data in XML | 6v49_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 6v49_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v49 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v49 | HTTPS FTP |
-Related structure data
Related structure data | 6v44C 6v46C 6v47C 6v48C 4m5gS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 36316.891 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)) Strain: A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9) Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q20ND8 #2: Protein | Mass: 20223.229 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)) Strain: A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9) Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q20ND8 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: 0.1M Sodium acetate trihydrate, pH5.0, 20% (v/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 57980 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.069 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 3096 / Rsym value: 0.608 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4m5g Resolution: 2.5→44.09 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 29.578 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.611 / ESU R Free: 0.304 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 230.53 Å2 / Biso mean: 70.255 Å2 / Biso min: 25.04 Å2
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Refinement step | Cycle: final / Resolution: 2.5→44.09 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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