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Yorodumi- PDB-2onw: Structure of SSTSSA, a fibril forming peptide from Bovine Pancrea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2onw | ||||||
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Title | Structure of SSTSSA, a fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A, residues 15-20) | ||||||
Components | fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A) | ||||||
Keywords | PROTEIN FIBRIL / parallel face-to-face-Up/Up beta sheets / steric zipper | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 | 2onw.cif.gz | 9.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2onw.ent.gz | 6.9 KB | Display | PDB format |
PDBx/mmJSON format | 2onw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2onw_validation.pdf.gz | 371.2 KB | Display | wwPDB validaton report |
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Full document | 2onw_full_validation.pdf.gz | 371.1 KB | Display | |
Data in XML | 2onw_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 2onw_validation.cif.gz | 2.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/2onw ftp://data.pdbj.org/pub/pdb/validation_reports/on/2onw | HTTPS FTP |
-Related structure data
Related structure data | 2okzC 2ol9C 2olxC 2ommC 2ompC 2omqC 2on9C 2onaC 2onvC 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. Each sheet is comprised of beta strands generated by unit cell translations along the y-axis. The second sheet in the pair-of-sheet structures is generated by applying the operator -x+1, y+1/2, -z+1/2. In the second sheet also, beta strands are generated by unit cell translations along the y-axis. |
-Components
#1: Protein/peptide | Mass: 522.508 Da / Num. of mol.: 1 / Fragment: hinge loop region (residues 15-20) / Source method: obtained synthetically / Details: The peptide SSTSAA was commercially synthesized. |
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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 grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Peptide concentration: 30 mg/ml, Reservoir: 0.1M HEPES-Na, pH 7.5, 10% v/v isopropanol, 20% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
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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: MARRESEARCH / Detector: CCD / Date: Jan 1, 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→80 Å / Num. obs: 474 / % possible obs: 89.3 % / Biso Wilson estimate: 6.599 Å2 / Rmerge(I) obs: 0.174 / Χ2: 1.067 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.5→1.62 Å / Rmerge(I) obs: 0.434 / Num. unique all: 98 / Χ2: 1.084 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5 residue beta strand SSTSA with the C-terminal alanine absent Resolution: 1.51→21 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.903 / SU B: 2.481 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.102 / 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: 5.291 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→21 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.551 Å / Total num. of bins used: 20
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