+Open data
-Basic information
Entry | Database: PDB / ID: 5e5z | ||||||
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Title | Structure of the amyloid forming peptide LVHSSN (residues | ||||||
Components | LVHSSN (residues 16-21) from islet amyloid polypeptide | ||||||
Keywords | de novo protein / membrane protein / amyloid-like protofibril / Protein Fibril | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.664 Å | ||||||
Authors | Soriaga, A.B. / Eisenberg, D. | ||||||
Citation | Journal: J.Phys.Chem.B / Year: 2016 Title: Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets. Authors: Soriaga, A.B. / Sangwan, S. / Macdonald, R. / Sawaya, M.R. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e5z.cif.gz | 10.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e5z.ent.gz | 5.5 KB | Display | PDB format |
PDBx/mmJSON format | 5e5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e5z_validation.pdf.gz | 400 KB | Display | wwPDB validaton report |
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Full document | 5e5z_full_validation.pdf.gz | 400 KB | Display | |
Data in XML | 5e5z_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 5e5z_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5z ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5z | 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: 656.709 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 |
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-Sample preparation
Crystal | Density Matthews: 1.32 Å3/Da / Density % sol: 6.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 20 mg/ml in water and mixed with 0.09 M HEPES pH 7.5, 1.26M tri-sodium citrate, and 10% glycerol |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 1136 / % possible obs: 92.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.664→9.459 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.27 / Stereochemistry target values: LS_WUNIT_K1
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Solvent computation | Shrinkage radii: 0 Å / VDW probe radii: 0 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 251.472 Å2 / ksol: 0.6 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.664→9.459 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6644→9.4587 Å
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Refinement TLS params. | Method: refined / Origin x: 4.5323 Å / Origin y: 0.1096 Å / Origin z: 3.976 Å
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Refinement TLS group | Selection details: all |