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Yorodumi- PDB-5sur: X-ray crystallographic structure of a covalent trimer derived fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5sur | ||||||
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Title | X-ray crystallographic structure of a covalent trimer derived from A-beta 17_36. Synchrotron data set. (ORN)CVF(MEA)CED(ORN)AIIGL(ORN)V. | ||||||
Components | 16mer A-beta peptide: ORN-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORN-ALA-ILE-ILE-GLY-LEU-ORN-VAL | ||||||
Keywords | DE NOVO PROTEIN / amyloid / oligomer / Alzheimer's / trimer / PROTEIN FIBRIL | ||||||
Function / homology | HEXANE-1,6-DIOL Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | ||||||
Authors | Kreutzer, A.G. / Yoo, S. / Nowick, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2017 Title: Stabilization, Assembly, and Toxicity of Trimers Derived from A beta. Authors: Kreutzer, A.G. / Yoo, S. / Spencer, R.K. / Nowick, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sur.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sur.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 5sur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/5sur ftp://data.pdbj.org/pub/pdb/validation_reports/su/5sur | HTTPS FTP |
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-Related structure data
Related structure data | 5susSC 5sutC 5suuC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 | x 6
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1785.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 16mer peptide derived from A-beta 17-36 / Source: (synth.) Homo sapiens (human) #2: Chemical | #3: Chemical | ChemComp-HEZ / #4: Chemical | #5: 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: 3.13 Å3/Da / Density % sol: 60.76 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris buffer at pH 7.83, 0.2 M MgCl2, 3.32 M 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.801→27.45 Å / Num. obs: 8947 / % possible obs: 99 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.01053 / Rsym value: 0.0149 / Net I/σ(I): 23.12 |
Reflection shell | Resolution: 1.801→1.866 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6542 / Mean I/σ(I) obs: 1.13 / CC1/2: 0.532 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5SUS Resolution: 1.801→27.45 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.801→27.45 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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