+Open data
-Basic information
Entry | Database: PDB / ID: 6c3s | ||||||
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Title | AMYLOID FORMING PEPTIDE YTIAAL FROM TRANSTHYRETIN | ||||||
Components | TYR-THR-ILE-ALA-ALA-LEU | ||||||
Keywords | PROTEIN FIBRIL / amyloid / transthyretin / fibril | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å | ||||||
Authors | Sievers, S.A. / Sawaya, M.R. / Saelices, L. / Eisenberg, D.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2018 Title: Crystal structures of amyloidogenic segments of human transthyretin. Authors: Saelices, L. / Sievers, S.A. / Sawaya, M.R. / Eisenberg, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c3s.cif.gz | 9.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c3s.ent.gz | 4.8 KB | Display | PDB format |
PDBx/mmJSON format | 6c3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c3s_validation.pdf.gz | 405.5 KB | Display | wwPDB validaton report |
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Full document | 6c3s_full_validation.pdf.gz | 405.5 KB | Display | |
Data in XML | 6c3s_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 6c3s_validation.cif.gz | 2.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/6c3s ftp://data.pdbj.org/pub/pdb/validation_reports/c3/6c3s | 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 650.764 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 | Density Matthews: 1.54 Å3/Da / Density % sol: 20.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: YTIAAL crystals were grown from a solution containing 10mg/mL peptide. The reservoir contained 100mM Bis-Tris pH 5.5 and 3 M sodium chloride. Crystals were soaked on 25% Glycerol, prior to diffraction |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.895432 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 13, 2007 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.895432 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→90 Å / Num. obs: 625 / % possible obs: 98.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 10.22 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.006 / Net I/σ(I): 9.6 / Num. measured all: 3501 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ideal beta strand Resolution: 1.602→22.398 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 28.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 28.35 Å2 / Biso mean: 13.43 Å2 / Biso min: 4.56 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.602→22.398 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6022→1.659 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
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