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Yorodumi- PDB-8ani: Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ani | ||||||||||||
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Title | Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 10% ethanol | ||||||||||||
Components | Peptide LYIQWL from Tc5b | ||||||||||||
Keywords | PROTEIN FIBRIL / amyloid | ||||||||||||
Function / homology | ETHANOL / trifluoroacetic acid Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||||||||
Authors | Durvanger, Z. | ||||||||||||
Funding support | Hungary, European Union, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation. Authors: Horvath, D. / Durvanger, Z. / K Menyhard, D. / Sulyok-Eiler, M. / Bencs, F. / Gyulai, G. / Horvath, P. / Taricska, N. / Perczel, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ani.cif.gz | 23.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ani.ent.gz | 13 KB | Display | PDB format |
PDBx/mmJSON format | 8ani.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ani_validation.pdf.gz | 398.1 KB | Display | wwPDB validaton report |
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Full document | 8ani_full_validation.pdf.gz | 398.1 KB | Display | |
Data in XML | 8ani_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 8ani_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/8ani ftp://data.pdbj.org/pub/pdb/validation_reports/an/8ani | HTTPS FTP |
-Related structure data
Related structure data | 8angC 8anhC 8anjC 8ankC 8anlC 8anmC 8annC 8onqC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: Chemical | ChemComp-TFA / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-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: 20.38 % |
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Crystal grow | Temperature: 293 K / Method: evaporation, recrystallization Details: Peptide was dissolved in 10% ethanol at 0.5 mg/ml concentration, then incubated at 293K overnight. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→18.76 Å / Num. obs: 2253 / % possible obs: 98.13 % / Redundancy: 4.93 % / Biso Wilson estimate: 5.6 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.168 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.35→1.4 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 214 / CC1/2: 0.756 / Rrim(I) all: 0.745 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: crystal structure of LYIQWL grown from acetonitrile/water Resolution: 1.35→18.76 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 8.6422 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 5.95 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→18.76 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.607611122042 Å / Origin y: 0.80800839191 Å / Origin z: 1.79779049102 Å
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Refinement TLS group | Selection details: all |