+Open data
-Basic information
Entry | Database: PDB / ID: 8anj | ||||||||||||
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Title | Structure of the amyloid-forming peptide DFINWL from human GLP-2 | ||||||||||||
Components | Peptide DFINWL from human GLP-2 | ||||||||||||
Keywords | PROTEIN FIBRIL / amyloid | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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 | 8anj.cif.gz | 12.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8anj.ent.gz | 5.6 KB | Display | PDB format |
PDBx/mmJSON format | 8anj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8anj_validation.pdf.gz | 371.7 KB | Display | wwPDB validaton report |
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Full document | 8anj_full_validation.pdf.gz | 371.6 KB | Display | |
Data in XML | 8anj_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 8anj_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/8anj ftp://data.pdbj.org/pub/pdb/validation_reports/an/8anj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 806.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 310 K / Method: evaporation, recrystallization Details: Lyophilized peptide was dissolved in 0.6 mg/ml concentration in a solution containing 30 % acetonitrile and 0.1 % TFA and incubated at 310K for 4 weeks. |
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-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: Nov 9, 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: 1.55→16.96 Å / Num. obs: 773 / % possible obs: 98.35 % / Redundancy: 2.88 % / Biso Wilson estimate: 12.69 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.067 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.55→1.61 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 77 / CC1/2: 0.921 / Rrim(I) all: 0.356 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: crystal structure of LYIQWL Resolution: 1.55→16.95 Å / SU ML: 0.0963 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.2751 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: 13.34 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→16.95 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→16.95 Å
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