+Open data
-Basic information
Entry | Database: PDB / ID: 5txh | ||||||
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Title | Polymorphic form 2 of amyloid-beta derived peptide - IFAEDV | ||||||
Components | IFAEDV | ||||||
Keywords | DE NOVO PROTEIN / protein fibril | ||||||
Function / homology | ISOPROPYL ALCOHOL Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Model details | amyloid fibril | ||||||
Authors | Sangwan, S. / Sawaya, M.R. / Eisenberg, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2018 Title: Distal amyloid beta-protein fragments template amyloid assembly. Authors: Do, T.D. / Sangwan, S. / de Almeida, N.E.C. / Ilitchev, A.I. / Giammona, M. / Sawaya, M.R. / Buratto, S.K. / Eisenberg, D.S. / Bowers, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5txh.cif.gz | 14.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5txh.ent.gz | 8.9 KB | Display | PDB format |
PDBx/mmJSON format | 5txh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/5txh ftp://data.pdbj.org/pub/pdb/validation_reports/tx/5txh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a pair of beta sheets with beta strands. As an example, the symmetry operators to generate a pair of sheets with 4 strands in each sheet is provided |
-Components
#1: Protein/peptide | Mass: 692.757 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-IPA / | #3: 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: 1.48 Å3/Da / Density % sol: 16.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Reservoir contained 20% PEG 4000, 0.1M Sodium Citrate pH 5.6 and 20% Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→29.23 Å / Num. obs: 3593 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 8.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5 residue beta strand Resolution: 1.45→29.23 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.986 / SU B: 0.96 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.058 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 36.63 Å2 / Biso mean: 7.477 Å2 / Biso min: 3.26 Å2
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Refinement step | Cycle: final / Resolution: 1.45→29.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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