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- PDB-8qww: Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qww | ||||||||||||
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Title | Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 10% ethanol without TFA | ||||||||||||
![]() | Peptide LYIQWL from Tc5b | ||||||||||||
![]() | PROTEIN FIBRIL / amyloid | ||||||||||||
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 KB | Display | ![]() |
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PDB format | ![]() | 11.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411.2 KB | Display | ![]() |
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Full document | ![]() | 411.2 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 2.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 835.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 310 K / Method: evaporation, recrystallization Details: The peptide was dissolved in 10 v/v% ethanol at 0.5 mg/ml concentration and incubated at 310K. |
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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: Jul 13, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.05 Å / Num. obs: 1372 / % possible obs: 97.93 % / Redundancy: 3.28 % / Biso Wilson estimate: 6.35 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.101 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 132 / CC1/2: 0.727 / Rrim(I) all: 0.567 / % possible all: 88 |
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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: 9.22 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→19.05 Å
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Refinement TLS params. | Method: refined / Origin x: 1.95823275698 Å / Origin y: 4.03530295693 Å / Origin z: 5.48028424488 Å
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Refinement TLS group | Selection details: all |