+Open data
-Basic information
Entry | Database: PDB / ID: 4uby | ||||||
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Title | Crystal structure of a polymorphic beta1 peptide | ||||||
Components | prion peptide | ||||||
Keywords | de novo protein / membrane protein / prion peptide | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / 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 | 4uby.cif.gz | 17.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uby.ent.gz | 11.4 KB | Display | PDB format |
PDBx/mmJSON format | 4uby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uby_validation.pdf.gz | 378.5 KB | Display | wwPDB validaton report |
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Full document | 4uby_full_validation.pdf.gz | 378.5 KB | Display | |
Data in XML | 4uby_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 4uby_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/4uby ftp://data.pdbj.org/pub/pdb/validation_reports/ub/4uby | HTTPS FTP |
-Related structure data
Related structure data | 4tutC 4ubzC 4w5lC 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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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: 564.633 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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: 1.66 Å3/Da / Density % sol: 25.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, and 2 M ammonium sulfate |
-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: 6346 / % possible obs: 80.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 2.67 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.016 / Net I/av σ(I): 16.26 / Net I/σ(I): 24.6 / Num. measured all: 18020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1→13.822 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 2.32 / Phase error: 16.86 / 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: 34.08 Å2 / Biso mean: 5.8555 Å2 / Biso min: 1.64 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1→13.822 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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