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- PDB-8qwv: Structure of the amyloid-forming peptide LYIQNL, grown in the pre... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qwv | ||||||||||||
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Title | Structure of the amyloid-forming peptide LYIQNL, grown in the presence of ethanol | ||||||||||||
![]() | Peptide LYIQNL | ||||||||||||
![]() | PROTEIN FIBRIL / amyloid | ||||||||||||
Function / homology | ETHANOL![]() | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Durvanger, Z. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Solvent induced amyloid polymorphism reveals the elusive class 3 topology Authors: Durvanger, Z. / Bencs, F. / Horvath, D. / Perczel, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.4 KB | Display | ![]() |
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PDB format | ![]() | 12.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.4 KB | Display | ![]() |
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Full document | ![]() | 429.4 KB | Display | |
Data in XML | ![]() | 2.9 KB | Display | |
Data in CIF | ![]() | 3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qwuC ![]() 8qwwC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 762.894 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: evaporation, recrystallization / pH: 4.8 Details: Peptide dissolved in 0.1M acetate (pH 4.80) at 0.15 mg/ml concentration was equilibrated against 60% ethanol |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.66 Å / Num. obs: 988 / % possible obs: 99.3 % / Redundancy: 2.83 % / Biso Wilson estimate: 10.67 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.147 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 82 / CC1/2: 0.415 / Rrim(I) all: 0.63 / % possible all: 92.13 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.77 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→19.66 Å
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Refinement TLS params. | Method: refined / Origin x: 0.62331674088 Å / Origin y: 0.487485497637 Å / Origin z: 6.00345622728 Å
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Refinement TLS group | Selection details: all |