+Open data
-Basic information
Entry | Database: PDB / ID: 2okz | ||||||
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Title | MVGGVV peptide derived from Alzheimer's A-beta | ||||||
Components | peptide from Alzheimer's A-beta | ||||||
Keywords | PROTEIN FIBRIL / steric zipper | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sawaya, M.R. / Sambashivan, S. / 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 | 2okz.cif.gz | 8.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2okz.ent.gz | 5.6 KB | Display | PDB format |
PDBx/mmJSON format | 2okz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/2okz ftp://data.pdbj.org/pub/pdb/validation_reports/ok/2okz | HTTPS FTP |
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-Related structure data
Related structure data | 2ol9C 2olxC 2ommC 2ompC 2omqC 2on9C 2onaC 2onvC 2onwC 2onxC 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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-Components
#1: Protein/peptide | Mass: 560.707 Da / Num. of mol.: 2 / Fragment: residues 35-40 / Source method: obtained synthetically Details: This sequence corresponds to residues 35-40 of human A-beta peptide |
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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: 4.6 Details: 0.2 M CaCl2, 20% isopropanol, 0.1 M Na acetate, pH 4.6, 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 | Monochromator: channel-cut Si-111 monochromator and an ellipsoidal mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9466 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→90 Å / Num. all: 650 / Num. obs: 650 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.158 / Χ2: 1.073 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 1.8→1.94 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.447 / Num. unique all: 123 / Χ2: 1.082 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MVGGVV from space group P1 Resolution: 1.8→23.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.396 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.177 / 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: 11.768 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→23.56 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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