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- PDB-2onx: NNQQ peptide corresponding to residues 8-11 of yeast prion sup35 ... -
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Open data
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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) | ||||||
![]() | peptide corresponding to residues 8-11 of yeast prion sup35 | ||||||
![]() | PROTEIN FIBRIL / steric zipper / beta sheets | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7.4 KB | Display | ![]() |
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PDB format | ![]() | 4.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 371.3 KB | Display | ![]() |
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Full document | ![]() | 371.3 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 2.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data |
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Links
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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. |
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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: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure: ![]() 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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