+Open data
-Basic information
Entry | Database: PDB / ID: 2olx | ||||||
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Title | Structure of NNQQ Peptide from Yeast Prion SUP35 | ||||||
Components | NNQQ peptide derived from Yeast Prion Sup35 | ||||||
Keywords | PROTEIN FIBRIL / steric zipper / glutamine zipper / polar zipper / asparagine zipper | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Nelson, R. / Sawaya, M.R. / Eisenberg, D. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A.O. / Riekel, C. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2olx.cif.gz | 8.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2olx.ent.gz | 5.5 KB | Display | PDB format |
PDBx/mmJSON format | 2olx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/2olx ftp://data.pdbj.org/pub/pdb/validation_reports/ol/2olx | HTTPS FTP |
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-Related structure data
Related structure data | 2okzC 2ol9C 2ommC 2ompC 2omqC 2on9C 2onaC 2onvC 2onwC 2onxC 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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Details | One sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the b axis. The second sheet of the steric zipper can be generated by application of the crystallographic operator -X,1/2+Y,1/2-Z, and repeated unit cell translations of this strand along the b axis. |
-Components
#1: Protein/peptide | Mass: 502.478 Da / Num. of mol.: 1 / Fragment: residues 8-11 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 19, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9466 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→90 Å / Num. all: 426 / Num. obs: 426 / % possible obs: 74.9 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.124 / Χ2: 1.072 / Net I/σ(I): 8.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: polyalanine ideal beta-strand Resolution: 1.42→15.28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.75 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.984 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→15.28 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.456 Å / Total num. of bins used: 20
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