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- PDB-6c88: STRUCTURE OF THE AMYLOID FORMING PEPTIDE VAVHVF FROM TRANSTHYRETIN -
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Open data
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Basic information
Entry | Database: PDB / ID: 6c88 | ||||||
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Title | STRUCTURE OF THE AMYLOID FORMING PEPTIDE VAVHVF FROM TRANSTHYRETIN | ||||||
![]() | VAL-ALA-VAL-HIS-VAL-PHE | ||||||
![]() | PROTEIN FIBRIL / amyloid / transthyretin / fibril | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saelices, L. / Sawaya, M.R. / Eisenberg, D.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of amyloidogenic segments of human transthyretin. Authors: Saelices, L. / Sievers, S.A. / Sawaya, M.R. / Eisenberg, D.S. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 11.7 KB | Display | ![]() |
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PDB format | ![]() | 6.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.3 KB | Display | ![]() |
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Full document | ![]() | 410.3 KB | Display | |
Data in XML | ![]() | 2.8 KB | Display | |
Data in CIF | ![]() | 2.9 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: 671.806 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 23.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10mg/ml peptide solution. Reservoir contained 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30% v/v 2-Propanol. Crystals were soaked in 25% glycerol prior to diffraction |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 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: 1.85→100 Å / Num. obs: 744 / % possible obs: 84.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 4.01 Å2 / Rmerge(I) obs: 0.28 / Χ2: 1.107 / Net I/σ(I): 3.1 / Num. measured all: 2837 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 23.47 Å2 / Biso mean: 3.7137 Å2 / Biso min: 0.34 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.851→18.365 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8506→1.917 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
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