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Yorodumi- PDB-8t82: Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms hetero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t82 | ||||||
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Title | Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms heterochiral rippled beta-sheet, includes pentafluoropropionic acid | ||||||
Components | amyloid beta segment 35-MVGGVV-40, racemic mixture | ||||||
Keywords | PROTEIN FIBRIL / Rippled beta sheet / amyloid fibril | ||||||
Function / homology | pentafluoropropanoic acid Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å | ||||||
Authors | Sawaya, M.R. / Raskatov, J.A. / Hazari, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Racemic Peptides from Amyloid beta and Amylin Form Rippled beta-Sheets Rather Than Pleated beta-Sheets. Authors: Hazari, A. / Sawaya, M.R. / Sajimon, M. / Vlahakis, N. / Rodriguez, J. / Eisenberg, D. / Raskatov, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t82.cif.gz | 12.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t82.ent.gz | 6.5 KB | Display | PDB format |
PDBx/mmJSON format | 8t82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t82_validation.pdf.gz | 693.1 KB | Display | wwPDB validaton report |
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Full document | 8t82_full_validation.pdf.gz | 693.1 KB | Display | |
Data in XML | 8t82_validation.xml.gz | 2.2 KB | Display | |
Data in CIF | 8t82_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/8t82 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/8t82 | HTTPS FTP |
-Related structure data
Related structure data | 8t84C 8t86C 8t89C 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: 560.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: Chemical | ChemComp-YWK / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.63 Å3/Da / Density % sol: 24.59 % / Description: needle-shaped |
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Crystal grow | Temperature: 298 K / Method: batch mode / Details: pentafluoropropionic acid, water |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→13.79 Å / Num. obs: 2485 / % possible obs: 82.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 47.8 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.107 / Net I/σ(I): 10.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.1→13.79 Å / SU ML: 0.0483 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.0567 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: 6.57 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→13.79 Å
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Refine LS restraints |
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LS refinement shell |
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