+Open data
-Basic information
Entry | Database: PDB / ID: 6udr | |||||||||
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Title | S2 symmetric peptide design number 3 crystal form 1, Lurch | |||||||||
Components | S2-3, Lurch crystal form 1 | |||||||||
Keywords | DE NOVO PROTEIN / cyclic peptide / centrosymmetric macrocycle / L and D-amino acids | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 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 | 6udr.cif.gz | 11.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6udr.ent.gz | 6.6 KB | Display | PDB format |
PDBx/mmJSON format | 6udr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/6udr ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6udr | HTTPS FTP |
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-Related structure data
Related structure data | 6ucxC 6ud9C 6udwC 6udzC 6uf4C 6uf7C 6uf8C 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
#1: Protein/peptide | Mass: 1215.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
Compound details | Crystallographic symmetry operator -x,-y,-z generates the C-terminal half of the cyclic peptide ...Crystallographic symmetry operator -x,-y,-z generates the C-terminal half of the cyclic peptide Q(DTH)(DAR)(DPR)(DAS) |
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 | Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M trisodium citrate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2018 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1→11.52 Å / Num. obs: 2461 / % possible obs: 75 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.08 / Rrim(I) all: 0.151 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.05→1.17 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.145 / Num. measured all: 1742 / Num. unique obs: 515 / CC1/2: 0.961 / Rpim(I) all: 0.095 / Rrim(I) all: 0.175 / Net I/σ(I) obs: 8 / % possible all: 62 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1→11.52 Å / SU ML: 0.0451 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 7.6413
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 1.44 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→11.52 Å /
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Refine LS restraints |
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LS refinement shell |
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