+Open data
-Basic information
Entry | Database: PDB / ID: 6ug2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | C2 symmetric peptide design number 1, Zappy, crystal form 2 | |||||||||
Components | C2-1, Zappy, crystal form 2 | |||||||||
Keywords | DE NOVO PROTEIN / cyclic peptide / 2-fold symmetric / L and D-amino acids | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 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
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ug2.cif.gz | 16.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ug2.ent.gz | 12.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ug2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/6ug2 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ug2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ucxC 6ud9C 6udrC 6udwC 6udzC 6uf4C 6uf7C 6uf8C 6uf9C 6ufaC 6ufuC 6ug3C 6ug6C 6ugbC 6ugcC C: citing same article (ref.) |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 1021.079 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Residue 1 is partially racemized. Both DSN and SER are present at this position. The racemization was an undesired side product of the peptide synthesis. Source: (synth.) synthetic construct (others) |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Compound details | Residue 1 is partially racemized. Both DSN and SER are present at this position. The racemization ...Residue 1 is partially racemized. Both DSN and SER are present at this position. The racemization was an undesired side product of the peptide synthesis. |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.55 Å3/Da / Density % sol: 20.86 % Description: needle, 200 microns long and less than 5 microns thick |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 28% (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2019 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→19.734 Å / Num. obs: 4357 / % possible obs: 87.4 % / Redundancy: 4.753 % / Biso Wilson estimate: 11.43 Å2 / Rmerge(I) obs: 0.25 / Net I/σ(I): 4.08 |
Reflection shell | Resolution: 1.1→1.13 Å / Redundancy: 4.06 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 240 / % possible all: 66.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.1→19.73 Å / SU ML: 0.077 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.01
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.18 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→19.73 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|