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Yorodumi- PDB-5f1w: Crystal structure of the enantiomer of a macrocyclic peptide cont... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f1w | ||||||
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Title | Crystal structure of the enantiomer of a macrocyclic peptide containing fragments from alpha synuclein 36-55 | ||||||
Components | Macrocyclic peptide | ||||||
Keywords | IMMUNE SYSTEM / beta-Hairpins | ||||||
Function / homology | polypeptide(D) / polypeptide(D) (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.161 Å | ||||||
Authors | Salveson, P.J. / Spencer, R.K. / Nowick, J.S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: X-ray Crystallographic Structure of Oligomers Formed by a Toxic beta-Hairpin Derived from alpha-Synuclein: Trimers and Higher-Order Oligomers. Authors: Salveson, P.J. / 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 | 5f1w.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f1w.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 5f1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f1w_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 5f1w_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 5f1w_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 5f1w_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/5f1w ftp://data.pdbj.org/pub/pdb/validation_reports/f1/5f1w | HTTPS FTP |
-Related structure data
Related structure data | 5f1tSC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Polypeptide(D) | Mass: 1724.804 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.7 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M HEPES (pH 8.0), 0.5 m ammonium sulphate, 34% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.997 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2015 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 2.161→34.842 Å / Num. obs: 8669 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 5.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F1T Resolution: 2.161→34.842 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.161→34.842 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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