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Yorodumi- PDB-2onv: Crystal Structure of the amyloid-fibril forming peptide GGVVIA de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2onv | ||||||
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Title | Crystal Structure of the amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta (Abeta37-42). | ||||||
Components | amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta | ||||||
Keywords | PROTEIN FIBRIL / steric zipper / beta sheets | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Sambashivan, S. / 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 | 2onv.cif.gz | 7.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2onv.ent.gz | 4.9 KB | Display | PDB format |
PDBx/mmJSON format | 2onv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2onv_validation.pdf.gz | 404.8 KB | Display | wwPDB validaton report |
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Full document | 2onv_full_validation.pdf.gz | 404.7 KB | Display | |
Data in XML | 2onv_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 2onv_validation.cif.gz | 2.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/2onv ftp://data.pdbj.org/pub/pdb/validation_reports/on/2onv | HTTPS FTP |
-Related structure data
Related structure data | 2okzC 2ol9C 2olxC 2ommC 2ompC 2omqC 2on9C 2onaC 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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Details | The biological unit is a pair of sheets. Beta strands within the sheet are generated by unit cell translations along the z-axis. The second sheet in the pair of sheets is generated by applying the symmetry operator x+1/2, -y+1/2, -z. Within the second sheet also, beta strands are generated by unit cell translations along the z-axis. |
-Components
#1: Protein/peptide | Mass: 514.616 Da / Num. of mol.: 1 / Fragment: residues 37-42 / Source method: obtained synthetically / Details: Peptide was commercially synthesized by CSBio. |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 23.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Peptide concentration: 15.0 mg/ml, Peptide:reservoir:additive ratio 5:4:1, Reservoir: 2.0M Ammonium sulfate, Additive: 3.0% 0.1M hexamine cobalt (III) chloride , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-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 17, 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: 1.6→90 Å / Num. obs: 532 / % possible obs: 96.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 15.962 Å2 / Rmerge(I) obs: 0.192 / Χ2: 1.085 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.6→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.42 / Num. unique all: 87 / Χ2: 1.102 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Extended beta strand GGVVIA Resolution: 1.61→20.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.852 / SU B: 4.479 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / 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: 9.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→20.57 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.653 Å / Total num. of bins used: 20
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