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Yorodumi- PDB-8yg2: Crystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Is... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8yg2 | ||||||
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Title | Crystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Islet Amyloid Polypeptide | ||||||
Components | Amyloidogenic peptide from Islet Amyloid Polypeptide | ||||||
Keywords | PROTEIN FIBRIL / Amyloid / CASL | ||||||
Function / homology | FORMIC ACID Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Sawazaki, T. / Sasaki, D. / Sohma, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yg2.cif.gz | 11.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yg2.ent.gz | 5.7 KB | Display | PDB format |
PDBx/mmJSON format | 8yg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/8yg2 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/8yg2 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) |
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#2: Chemical | ChemComp-FMT / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.04 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→20.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.881 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.069
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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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