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- PDB-6ya2: Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ya2 | ||||||
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Title | Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated) | ||||||
![]() | Glycoprotein | ||||||
![]() | VIRAL PROTEIN / Envelope protein / attachment / viral entry / receptor binding / viral assembly | ||||||
Function / homology | ![]() modulation by virus of host process / host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dessau, M. / Bahat, Y. | ||||||
![]() | ![]() Title: Crystal structure of tomato spotted wilt virus G N reveals a dimer complex formation and evolutionary link to animal-infecting viruses Authors: Bahat, Y. / Alter, J. / Dessau, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.3 KB | Display | ![]() |
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PDB format | ![]() | 190.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y9lC ![]() 6y9mC ![]() 6ya0SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 21939.869 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: This construct is a S214C mutant construct based on 6YA0 entry. Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 19% PEG 8,000 (w/v) 0.1 M tris pH 7.5 0.2 M magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 26, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→18.85 Å / Num. obs: 24477 / % possible obs: 98.5 % / Redundancy: 6.976 % / Biso Wilson estimate: 67.877 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.108 / Χ2: 1.026 / Net I/σ(I): 13.14 / Num. measured all: 170741 / Scaling rejects: 32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YA0 Resolution: 2.5→18.85 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 203.65 Å2 / Biso mean: 75.2674 Å2 / Biso min: 16.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→18.85 Å
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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 / Origin x: -13.7352 Å / Origin y: -8.7137 Å / Origin z: 4.6998 Å
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Refinement TLS group |
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