+
Open data
-
Basic information
Entry | Database: PDB / ID: 4w5p | ||||||
---|---|---|---|---|---|---|---|
Title | Prp peptide | ||||||
![]() | PrP 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 14.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 8.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 389.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 389.3 KB | Display | |
Data in XML | ![]() | 2.8 KB | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tutC ![]() 4ubyC ![]() 4ubzC ![]() 4w5lC ![]() 4w5mC ![]() 4w5yC ![]() 4w67C ![]() 4w71C ![]() 4wbuC ![]() 4wbvC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
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. |
-
Components
#1: Protein/peptide | Mass: 651.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MPD / ( | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.49 Å3/Da / Density % sol: 17.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-tris, 0.1 M ammonium acetate, and 40 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→50 Å / Num. obs: 2529 / % possible obs: 90.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.119 / Χ2: 1.003 / Net I/av σ(I): 11.412 / Net I/σ(I): 7.4 / Num. measured all: 10485 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.151→19.492 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.36 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 23.35 Å2 / Biso mean: 9.4231 Å2 / Biso min: 4.53 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.151→19.492 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.1508→19.4946 Å / Total num. of bins used: 1
|