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Yorodumi- PDB-6vas: Assembly of VIQKI I454(beta-L-homoisoleucine)with human parainflu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vas | |||||||||
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Title | Assembly of VIQKI I454(beta-L-homoisoleucine)with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain | |||||||||
Components | (Fusion glycoprotein F0) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Fusion glycoprotein / six-helix bundle / foldamer | |||||||||
Function / homology | Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0 Function and homology information | |||||||||
Biological species | Human parainfluenza 3 virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | |||||||||
Authors | Outlaw, V.K. / Gellman, S.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Infect Dis. / Year: 2020 Title: Effects of Single alpha-to-beta Residue Replacements on Recognition of an Extended Segment in a Viral Fusion Protein. Authors: Outlaw, V.K. / Kreitler, D.F. / Stelitano, D. / Porotto, M. / Moscona, A. / Gellman, S.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vas.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vas.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/6vas ftp://data.pdbj.org/pub/pdb/validation_reports/va/6vas | HTTPS FTP |
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-Related structure data
Related structure data | 6prlC 6pyqC 6pz6C 6v3vC 6nroS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 5656.473 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Human parainfluenza 3 virus (strain Wash/47885/57) References: UniProt: P06828 #2: Protein/peptide | Mass: 4208.922 Da / Num. of mol.: 2 Mutation: I454(beta-3-homoisoleucine), E459V, A463I, D466Q, Q479K, K480I Source method: obtained synthetically Source: (synth.) Human parainfluenza 3 virus (strain Wash/47885/57) References: UniProt: P06828 #3: 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: 1.43 Å3/Da / Density % sol: 13.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM imidazole/MES monohydrate (pH 6.5), 12.5% PEG1000, 12.5% PEG3350, 12.5% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→28.73 Å / Num. obs: 18936 / % possible obs: 99.65 % / Redundancy: 21.1 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.0238 / Rrim(I) all: 0.108 / Rsym value: 0.105 / Net I/σ(I): 15.96 |
Reflection shell | Resolution: 1.49→1.543 Å / Redundancy: 21.7 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 1814 / CC1/2: 0.682 / Rpim(I) all: 0.4476 / Rrim(I) all: 2.094 / Rsym value: 2.045 / % possible all: 98.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NRO Resolution: 1.49→28.73 Å / SU ML: 0.1972 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5046
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→28.73 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: -2.64466390231 Å / Origin y: 17.8902543259 Å / Origin z: 33.9777944271 Å
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Refinement TLS group | Selection details: all |