+Open data
-Basic information
Entry | Database: PDB / ID: 6uf8 | |||||||||
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Title | S2 symmetric peptide design number 6, London Bridge | |||||||||
Components | S2-6, London Bridge | |||||||||
Keywords | DE NOVO PROTEIN / cyclic peptide / centrosymmetric macrocycle / L- and D-amino acids | |||||||||
Function / homology | polypeptide(D) / polypeptide(D) (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.8 Å | |||||||||
Model details | S2 symmetric cyclic peptide | |||||||||
Authors | Mulligan, V.K. / Kang, C.S. / Antselovich, I. / Sawaya, M.R. / Yeates, T.O. / Baker, D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Computational design of mixed chirality peptide macrocycles with internal symmetry. Authors: Mulligan, V.K. / Kang, C.S. / Sawaya, M.R. / Rettie, S. / Li, X. / Antselovich, I. / Craven, T.W. / Watkins, A.M. / Labonte, J.W. / DiMaio, F. / Yeates, T.O. / Baker, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uf8.cif.gz | 15.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uf8.ent.gz | 9.8 KB | Display | PDB format |
PDBx/mmJSON format | 6uf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/6uf8 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/6uf8 | HTTPS FTP |
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-Related structure data
Related structure data | 6ucxC 6ud9C 6udrC 6udwC 6udzC 6uf4C 6uf7C 6uf9C 6ufaC 6ufuC 6ug2C 6ug3C 6ug6C 6ugbC 6ugcC 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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Components on special symmetry positions |
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-Components
#1: Polypeptide(D) | Mass: 1374.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ab initio design / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
Compound details | The asymmetric unit contains half of the molecule. The second half is generated by a ...The asymmetric unit contains half of the molecule. The second half is generated by a crystallographic symmetry operator. |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 0.1 M phosphate/citrate pH 4.2, 40% (v/v) PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.8856 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.8→18.93 Å / Num. obs: 10306 / % possible obs: 96.1 % / Redundancy: 5.695 % / Biso Wilson estimate: 9.919 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Χ2: 1.062 / Net I/σ(I): 18.88 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.8→16.36 Å / SU ML: 0.0591 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.2647
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.8→16.36 Å
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Refine LS restraints |
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LS refinement shell |
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