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- PDB-8yg2: Crystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Is... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yg2 | ||||||
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Title | Crystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Islet Amyloid Polypeptide | ||||||
![]() | Amyloidogenic peptide from Islet Amyloid Polypeptide | ||||||
![]() | PROTEIN FIBRIL / Amyloid / CASL | ||||||
Function / homology | FORMIC ACID![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sawazaki, T. / Sasaki, D. / Sohma, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Catalysis driven by an amyloid-substrate complex. Authors: Sawazaki, T. / Sasaki, D. / Sohma, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 11.7 KB | Display | ![]() |
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PDB format | ![]() | 5.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.2 KB | Display | ![]() |
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Full document | ![]() | 416.1 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 2.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 715.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Chemical | ChemComp-FMT / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.54 Å3/Da / Density % sol: 15.15 % / Description: Needle |
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Crystal grow | Temperature: 298 K / Method: evaporation / Details: Formic acid / PH range: 2.0-3.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→20.47 Å / Num. obs: 1063 / % possible obs: 91.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 59.11 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 2 % / Rmerge(I) obs: 0.155 / Num. unique obs: 55 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 5.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→20.47 Å /
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Refine LS restraints |
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