+Open data
-Basic information
Entry | Database: PDB / ID: 3fod | ||||||
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Title | AILSST segment from Islet Amyloid Polypeptide | ||||||
Components | AILSST hexapeptide segment from Islet Amyloid Polypeptide | ||||||
Keywords | PROTEIN FIBRIL / amyloid-like beta strand | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Wiltzius, J.J.W. / Sawaya, M.R. / Rajashankar, K. / Eisenberg, D. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Molecular mechanisms for protein-encoded inheritance. Authors: Wiltzius, J.J. / Landau, M. / Nelson, R. / Sawaya, M.R. / Apostol, M.I. / Goldschmidt, L. / Soriaga, A.B. / Cascio, D. / Rajashankar, K. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fod.cif.gz | 16.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fod.ent.gz | 12 KB | Display | PDB format |
PDBx/mmJSON format | 3fod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fod_validation.pdf.gz | 386.1 KB | Display | wwPDB validaton report |
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Full document | 3fod_full_validation.pdf.gz | 386 KB | Display | |
Data in XML | 3fod_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 3fod_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/3fod ftp://data.pdbj.org/pub/pdb/validation_reports/fo/3fod | HTTPS FTP |
-Related structure data
Related structure data | 3fpoC 3fr1C 3fthC 3ftkC 3ftlC 3ftrC 3fvaC 4np8C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 590.668 Da / Num. of mol.: 8 / Fragment: AILSST residues 25-30 / Source method: obtained synthetically Details: residues 25-30 (AILSST) from human Islet Amyloid Polypeptide, synthesized #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 | Density Matthews: 1.7 Å3/Da / Density % sol: 28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: reservoir contained 0.2M magnesium nitrate, 20% PEG3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→43.31 Å / Num. all: 5268 / Num. obs: 5268 / % possible obs: 84.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2 / Num. unique all: 518 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ideal beta strand Resolution: 1.4→43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.673 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.121 / ESU R Free: 0.118 / 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: 8.131 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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