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Yorodumi- PDB-2omp: LYQLEN peptide derived from human insulin chain A, residues 13-18 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2omp | ||||||
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Title | LYQLEN peptide derived from human insulin chain A, residues 13-18 | ||||||
Components | LYQLEN peptide derived from human insulin chain A, residues 13-18 | ||||||
Keywords | PROTEIN FIBRIL / steric zipper / antiparallel beta-sheet | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ivanova, M.I. / 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 | 2omp.cif.gz | 10.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2omp.ent.gz | 6.9 KB | Display | PDB format |
PDBx/mmJSON format | 2omp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/2omp ftp://data.pdbj.org/pub/pdb/validation_reports/om/2omp | HTTPS FTP |
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-Related structure data
Related structure data | 2okzC 2ol9C 2olxC 2ommC 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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Details | One sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the a axis. The second sheet of the steric zipper can be generated by application of the crystallographic operator X,Y,Z+1, and repeated unit cell translations of this strand along the a axis. |
-Components
#1: Protein/peptide | Mass: 778.850 Da / Num. of mol.: 2 / Fragment: residues 13-18 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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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: 310 K / Method: vapor diffusion, hanging drop / pH: 2.5 Details: 20mM peptide in 100 mM NaCl and 50 mM phosphate, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
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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: 1.8→90 Å / Num. obs: 752 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.186 / Χ2: 1.11 / Net I/σ(I): 4.8 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: idealized beta strands, polyalanine Resolution: 1.9→17.24 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.81 / SU B: 9.051 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.196 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 5.283 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→17.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 6 / Label seq-ID: 1 - 6
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