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Yorodumi- PDB-6v44: The crystal structure of hemagglutinin from swine influenza virus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v44 | |||||||||
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Title | The crystal structure of hemagglutinin from swine influenza virus A/swine/Missouri/A01727926/2015 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza virus / swine / H4 | |||||||||
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: 2.2 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 | 6v44.cif.gz | 603.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v44.ent.gz | 496.5 KB | Display | PDB format |
PDBx/mmJSON format | 6v44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v44_validation.pdf.gz | 502.4 KB | Display | wwPDB validaton report |
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Full document | 6v44_full_validation.pdf.gz | 508.4 KB | Display | |
Data in XML | 6v44_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 6v44_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v44 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v44 | HTTPS FTP |
-Related structure data
Related structure data | 6v46C 6v47C 6v48C 6v49C 5xl2S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 36651.152 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/swine/Missouri/A01727926/2015(H4N6)) Strain: A/swine/Missouri/A01727926/2015(H4N6) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A140D8S6 #2: Protein | Mass: 21442.586 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/swine/Missouri/A01727926/2015(H4N6)) Strain: A/swine/Missouri/A01727926/2015(H4N6) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A140D8S6 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Water | ChemComp-HOH / | 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: 2.84 Å3/Da / Density % sol: 56.69 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: 0.1M Tris-HCl, pH8.5, 30% (w/v) PEG 1000 |
-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: Jun 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 95268 / % possible obs: 98 % / Redundancy: 3.3 % / Rsym value: 0.087 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 2.2→2.26 Å / Num. unique obs: 8895 / Rsym value: 0.474 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XL2 Resolution: 2.2→33.207 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160.88 Å2 / Biso mean: 50.7893 Å2 / Biso min: 25.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→33.207 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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