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Yorodumi- PDB-2onx: NNQQ peptide corresponding to residues 8-11 of yeast prion sup35 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2onx | ||||||
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Title | NNQQ peptide corresponding to residues 8-11 of yeast prion sup35 (alternate crystal form) | ||||||
Components | peptide corresponding to residues 8-11 of yeast prion sup35 | ||||||
Keywords | PROTEIN FIBRIL / steric zipper / beta sheets | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H. ...Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H. / Madsen, A.O. / Riekel, C. / 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 | 2onx.cif.gz | 7.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2onx.ent.gz | 4.8 KB | Display | PDB format |
PDBx/mmJSON format | 2onx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/2onx ftp://data.pdbj.org/pub/pdb/validation_reports/on/2onx | HTTPS FTP |
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-Related structure data
Related structure data | 2okzC 2ol9C 2olxC 2ommC 2ompC 2omqC 2on9C 2onaC 2onvC 2onwC 1yjpS S: Starting model for refinement 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 | One sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the "a" unit cell dimension. The second sheet of the steric zipper can be generated by application of the crystallographic operator -X,1/2+Y,1-Z, and repeated unit cell translations of this strand along the "a" unit cell dimension. |
-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 / pH: 5.6 Details: 30-50 mg/mL peptide disolved in water and mixed with an equal volume of reservoir solution consisting of 100 mM trisodium citrate, 20% polyethylene glycol 4000 and 20% isopropanol, pH 5.6, ...Details: 30-50 mg/mL peptide disolved in water and mixed with an equal volume of reservoir solution consisting of 100 mM trisodium citrate, 20% polyethylene glycol 4000 and 20% isopropanol, pH 5.6, 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: Jul 16, 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: 1.5→90 Å / Num. obs: 259 / % possible obs: 63.8 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.152 / Χ2: 1.15 / Net I/σ(I): 10.1 | ||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1yjp Resolution: 1.52→15.43 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.275 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.146 / 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: 12.236 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→15.43 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.563 Å / Total num. of bins used: 20
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