+Open data
-Basic information
Entry | Database: PDB / ID: 6c4o | ||||||
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Title | AMYLOID FORMING PEPTIDE TIAALLS FROM TRANSTHYRETIN | ||||||
Components | THR-ILE-ALA-ALA-LEU-LEU-SER | ||||||
Keywords | PROTEIN FIBRIL / amyloid / transthyretin / fibril | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 | 6c4o.cif.gz | 11 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c4o.ent.gz | 6 KB | Display | PDB format |
PDBx/mmJSON format | 6c4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c4o_validation.pdf.gz | 375 KB | Display | wwPDB validaton report |
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Full document | 6c4o_full_validation.pdf.gz | 375.1 KB | Display | |
Data in XML | 6c4o_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 6c4o_validation.cif.gz | 2.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/6c4o ftp://data.pdbj.org/pub/pdb/validation_reports/c4/6c4o | 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: 687.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Water | ChemComp-HOH / | |
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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: 1.5 Å3/Da / Density % sol: 18.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: TIAALLS crystals were grown from 5mg/mL peptide and 10% acetonitrile. The reservoir contained 100mM Tris pH 8.5 and 0.3 M magnesium formate dihydrate. 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: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2017 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→90 Å / Num. obs: 784 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.217 / Χ2: 1.079 / Net I/σ(I): 4.4 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→14.21 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.189 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 35.06 Å2 / Biso mean: 6.636 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 1.79→14.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.794→1.839 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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