+Open data
-Basic information
Entry | Database: PDB / ID: 4w5m | ||||||
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Title | Prp peptide | ||||||
Components | PrP peptide | ||||||
Keywords | de novo protein / membrane protein / prion peptide | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 | 4w5m.cif.gz | 14.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w5m.ent.gz | 8.4 KB | Display | PDB format |
PDBx/mmJSON format | 4w5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w5m_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 4w5m_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 4w5m_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 4w5m_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/4w5m ftp://data.pdbj.org/pub/pdb/validation_reports/w5/4w5m | HTTPS FTP |
-Related structure data
Related structure data | 4tutC 4ubyC 4ubzC 4w5lC 4w5pC 4w5yC 4w67C 4w71C 4wbuC 4wbvC C: citing same article (ref.) |
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-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: 683.776 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MPD / ( | #3: 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: 1.85 Å3/Da / Density % sol: 33.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-tris, 2% 2-methyl-2,4-pentanediol (MPD), and 1.1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 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: 1.2→50 Å / Num. obs: 2911 / % possible obs: 86.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.071 / Χ2: 1.026 / Net I/av σ(I): 12.776 / Net I/σ(I): 11.1 / Num. measured all: 7028 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→23.644 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.53 / 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: 44.55 Å2 / Biso mean: 17.1338 Å2 / Biso min: 6.02 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→23.644 Å
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