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Open data
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Basic information
Entry | Database: PDB / ID: 3hak | ||||||
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Title | Human prion protein variant V129 | ||||||
![]() | Major prion protein | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, S. / Antony, L. / Hartmann, R. / Knaus, K.J. / Surewicz, K. / Surewicz, W.K. / Yee, V.C. | ||||||
![]() | ![]() Title: Conformational diversity in prion protein variants influences intermolecular beta-sheet formation. Authors: Lee, S. / Antony, L. / Hartmann, R. / Knaus, K.J. / Surewicz, K. / Surewicz, W.K. / Yee, V.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.2 KB | Display | ![]() |
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PDB format | ![]() | 24.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hafC ![]() 3heqC ![]() 3herC ![]() 3hesC ![]() 3hj5C ![]() 3hjxC C: citing same article ( |
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Similar 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
#1: Protein | Mass: 12370.712 Da / Num. of mol.: 1 / Fragment: UNP residues 125-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
Sequence details | THE COMPLETE SEQUENCE OF THE PROTEIN USED FOR CRYSTALLIZATION WAS: ...THE COMPLETE SEQUENCE OF THE PROTEIN USED FOR CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.9 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 0.1M Na/K phosphate, 20% PEG4K, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. obs: 8871 / % possible obs: 99.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.042 / Χ2: 0.99 / Net I/σ(I): 30.755 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.34 Å2 / Biso mean: 20.286 Å2 / Biso min: 9.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→16.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.798→1.844 Å / Total num. of bins used: 20
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