+Open data
-Basic information
Entry | Database: PDB / ID: 4w5l | ||||||
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Title | Crystal structure of a prp peptide | ||||||
Components | PrP peptide | ||||||
Keywords | de novo protein / membrane protein / prion peptide | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å | ||||||
Authors | Yu, L. / Lee, S.-J. / Yee, V. | ||||||
Citation | Journal: Biochemistry / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w5l.cif.gz | 14.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w5l.ent.gz | 8.6 KB | Display | PDB format |
PDBx/mmJSON format | 4w5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w5l_validation.pdf.gz | 405.8 KB | Display | wwPDB validaton report |
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Full document | 4w5l_full_validation.pdf.gz | 405.7 KB | Display | |
Data in XML | 4w5l_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 4w5l_validation.cif.gz | 3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/4w5l ftp://data.pdbj.org/pub/pdb/validation_reports/w5/4w5l | HTTPS FTP |
-Related structure data
Related structure data | 4tutC 4ubyC 4ubzC 4w5mC 4w5pC 4w5yC 4w67C 4w71C 4wbuC 4wbvC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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. |
-Components
#1: Protein/peptide | Mass: 665.738 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M tri-sodium citrate, 0.1 M Hepes pH 7.5, and 30 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.7749 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 4814 / % possible obs: 80.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 5.63 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.002 / Net I/av σ(I): 16.97 / Net I/σ(I): 14.6 / Num. measured all: 15931 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1→13.159 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 20.95 / 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: 47.42 Å2 / Biso mean: 10.077 Å2 / Biso min: 3.08 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1→13.159 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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