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- PDB-4ma8: Crystal structure of mouse prion protein complexed with Chlorpromazine -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ma8 | ||||||
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Title | Crystal structure of mouse prion protein complexed with Chlorpromazine | ||||||
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Function / homology | ![]() Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baral, P.K. / Swayampakula, M. / James, M.N.G. | ||||||
![]() | ![]() Title: Structural basis of prion inhibition by phenothiazine compounds. Authors: Baral, P.K. / Swayampakula, M. / Rout, M.K. / Kav, N.N. / Spyracopoulos, L. / Aguzzi, A. / James, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.7 KB | Display | ![]() |
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PDB format | ![]() | 192.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ma7C ![]() 4h88S C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 13360.877 Da / Num. of mol.: 1 / Fragment: UNP residues 116-229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23397.078 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Details: hybridoma / Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 23509.701 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Details: hybridoma / Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-Z80 / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.73 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→50 Å / Num. obs: 32491 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.5 / % possible all: 86.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4H88 Resolution: 2.2→34.99 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.02 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.404 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→34.99 Å
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Refine LS restraints |
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