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- PDB-6c3t: AMYLOID FORMING PEPTIDE AADTWE FROM TRANSTHYRETIN WITH ATTR-D38A ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6c3t | ||||||
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Title | AMYLOID FORMING PEPTIDE AADTWE FROM TRANSTHYRETIN WITH ATTR-D38A MUTATION ASSOCIATED WITH A FAMILIAL FORM OF TRANSTHYRETIN AMYLOIDOSIS | ||||||
![]() | ALA-ALA-ASP-THR-TRP-GLU | ||||||
![]() | PROTEIN FIBRIL / amyloid / transthyretin / fibril | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sievers, S.A. / Sawaya, M.R. / Saelices, L. / Eisenberg, D.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 13.5 KB | Display | ![]() |
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PDB format | ![]() | 8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.9 KB | Display | ![]() |
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Full document | ![]() | 370.9 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 2.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 691.686 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: AADTWE crystals were grown from a solution containing 100 mg/ml peptide. The reservoir contained 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, and 50 % v/v MPD. Crystals were soaked ...Details: AADTWE crystals were grown from a solution containing 100 mg/ml peptide. The reservoir contained 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, and 50 % v/v MPD. Crystals were soaked on 25% Glycerol prior to diffraction |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2008 | ||||||||||||||||||||||||||||||||||||||||||
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→90 Å / Num. obs: 3204 / % possible obs: 83.5 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.128 / Χ2: 1.071 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Ideal beta strand Resolution: 1→21.58 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.639 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.026 / 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: 32.14 Å2 / Biso mean: 3.311 Å2 / Biso min: 2.15 Å2
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Refinement step | Cycle: final / Resolution: 1→21.58 Å
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LS refinement shell | Resolution: 0.996→1.022 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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