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- PDB-6cg4: Covalently crosslinked trimer of a macrocyclic peptide derived fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cg4 | ||||||
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Title | Covalently crosslinked trimer of a macrocyclic peptide derived from Abeta(17-36) - (ORN)LCVFFCED(ORN)AII(2-nitrobenzylglycine)L(ORN)V | ||||||
![]() | ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL | ||||||
![]() | NEUROPEPTIDE / Amyloid / oligomer / Alzheimer's Disease / Abeta | ||||||
Function / homology | IODIDE ION![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() | ||||||
![]() | Salveson, P.J. / Nowick, J.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Controlling the Oligomerization State of A beta-Derived Peptides with Light. Authors: Salveson, P.J. / Haerianardakani, S. / Thuy-Boun, A. / Kreutzer, A.G. / Nowick, J.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 | ![]() | 41 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.4 KB | Display | ![]() |
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Full document | ![]() | 445.7 KB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 5.9 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 1906.272 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-MPD / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate pH 4.5 0.2 M sodium chloride 28% 2-methyl-2,4-pentanediol 0.1 M potassium iodide |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Dec 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→32.8 Å / Num. obs: 5269 / % possible obs: 100 % / Redundancy: 28.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 33.1 |
Reflection shell | Resolution: 2.03→2.08 Å / Rmerge(I) obs: 0.241 / CC1/2: 0.994 |
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Processing
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Refinement | Resolution: 2.083→32.783 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.083→32.783 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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