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Open data
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Basic information
Entry | Database: PDB / ID: 4ubz | ||||||
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Title | Crystal structure of a prion peptide | ||||||
![]() | prion peptide | ||||||
![]() | de novo protein / membrane protein / prion peptide | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Yu, L. / Lee, S.-J. / Yee, V. | ||||||
![]() | ![]() Title: Crystal Structures of Polymorphic Prion Protein beta 1 Peptides Reveal Variable Steric Zipper Conformations. Authors: Yu, L. / Lee, S.J. / 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 | ![]() | 13.4 KB | Display | ![]() |
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PDB format | ![]() | 7.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373.2 KB | Display | ![]() |
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Full document | ![]() | 373.2 KB | Display | |
Data in XML | ![]() | 2.6 KB | Display | |
Data in CIF | ![]() | 2.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tutC ![]() 4ubyC ![]() 4w5lC ![]() 4w5mC ![]() 4w5pC ![]() 4w5yC ![]() 4w67C ![]() 4w71C ![]() 4wbuC ![]() 4wbvC 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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1 | ![]()
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Unit cell |
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Details | BIOLOGICAL UNIT DISPLAYS ONLY A PORTION OF THE CRYSTAL LATTICE TO DEMONSTRATE THE CRYSTAL PACKING CONTENT. THE CRYSTAL PACKING IS FORMED BY A REPETITION IN BOTH DIRECTIONS OF THE PORTION INDICATED IN REMARK 350. |
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Components
#1: Protein/peptide | Mass: 578.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 21.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2 M sodium thiocyanate and 2.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1→50 Å / Num. obs: 3289 / % possible obs: 83.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 2.56 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.227 / Net I/av σ(I): 15.454 / Net I/σ(I): 14.4 / Num. measured all: 9659 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.001→12.476 Å / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 2.15 / Phase error: 8.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 7.11 Å2 / Biso mean: 2.7193 Å2 / Biso min: 1.39 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.001→12.476 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.001→12.4773 Å / Total num. of bins used: 1
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