+Open data
-Basic information
Entry | Database: PDB / ID: 6c3f | ||||||
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Title | AMYLOID FORMING PEPTIDE IYKVEI FROM TRANSTHYRETIN | ||||||
Components | ILE-TYR-LYS-VAL-GLU-ILE | ||||||
Keywords | PROTEIN FIBRIL / amyloid / transthyretin / fibril | ||||||
Function / homology | trifluoroacetic acid Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å | ||||||
Authors | Saelices, L. / Sawaya, M.R. / Eisenberg, D.S. | ||||||
Funding support | United States, 1items
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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. #1: Journal: J. Biol. Chem. / Year: 2015 Title: Uncovering the Mechanism of Aggregation of Human Transthyretin. Authors: Saelices, L. / Johnson, L.M. / Liang, W.Y. / Sawaya, M.R. / Cascio, D. / Ruchala, P. / Whitelegge, J. / Jiang, L. / Riek, 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 | 6c3f.cif.gz | 12.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c3f.ent.gz | 6.2 KB | Display | PDB format |
PDBx/mmJSON format | 6c3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c3f_validation.pdf.gz | 287.5 KB | Display | wwPDB validaton report |
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Full document | 6c3f_full_validation.pdf.gz | 287.5 KB | Display | |
Data in XML | 6c3f_validation.xml.gz | 2.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/6c3f ftp://data.pdbj.org/pub/pdb/validation_reports/c3/6c3f | 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: 764.929 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-TFA / | #3: 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: 1.47 Å3/Da / Density % sol: 16.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.5 M NaCl, 10 % v/v ethanol, 25% Glycerol |
-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: Feb 28, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.499→15.952 Å / Num. obs: 1413 / % possible obs: 96.3 % / Redundancy: 2.735 % / Biso Wilson estimate: 5.02 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.188 / Χ2: 0.974 / Net I/σ(I): 5.06 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.499→15.952 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 17.89 Å2 / Biso mean: 8.12 Å2 / Biso min: 2.21 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.499→15.952 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4991→1.553 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
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