+Open data
-Basic information
Entry | Database: PDB / ID: 7ucp | ||||||
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Title | computationally designed macrocycle | ||||||
Components | computationally designed cyclic peptide D8.3.p2 | ||||||
Keywords | DE NOVO PROTEIN / D8.3.p2 / cyclic peptide | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.85 Å | ||||||
Authors | Bhardwaj, G. / Baker, D. / Rettie, S. / Glynn, C. / Sawaya, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2022 Title: Accurate de novo design of membrane-traversing macrocycles. Authors: Bhardwaj, G. / O'Connor, J. / Rettie, S. / Huang, Y.H. / Ramelot, T.A. / Mulligan, V.K. / Alpkilic, G.G. / Palmer, J. / Bera, A.K. / Bick, M.J. / Di Piazza, M. / Li, X. / Hosseinzadeh, P. / ...Authors: Bhardwaj, G. / O'Connor, J. / Rettie, S. / Huang, Y.H. / Ramelot, T.A. / Mulligan, V.K. / Alpkilic, G.G. / Palmer, J. / Bera, A.K. / Bick, M.J. / Di Piazza, M. / Li, X. / Hosseinzadeh, P. / Craven, T.W. / Tejero, R. / Lauko, A. / Choi, R. / Glynn, C. / Dong, L. / Griffin, R. / van Voorhis, W.C. / Rodriguez, J. / Stewart, L. / Montelione, G.T. / Craik, D. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ucp.cif.gz | 18.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ucp.ent.gz | 13.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ucp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ucp_validation.pdf.gz | 406.8 KB | Display | wwPDB validaton report |
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Full document | 7ucp_full_validation.pdf.gz | 406.7 KB | Display | |
Data in XML | 7ucp_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 7ucp_validation.cif.gz | 2.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/7ucp ftp://data.pdbj.org/pub/pdb/validation_reports/uc/7ucp | HTTPS FTP |
-Related structure data
Related structure data | 7ubcC 7ubdC 7ubeC 7ubfC 7ubgC 7ubhC 7ubiC 7uzlC 8ctoC 8cunC 8cwaC C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 905.217 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Designed target sequence: Leu Val D-Pro MLE Leu Ile D-Pro MLE Peptide is N to C cyclized. Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
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: 1.43 Å3/Da |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1mg/ml peptide in acetonitrile |
-Data collection
Diffraction | Mean temperature: 196 K / Ambient temp details: LN2 gas / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.8377 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8377 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→100 Å / Num. obs: 8258 / % possible obs: 92.3 % / Redundancy: 4.96 % / Biso Wilson estimate: 47.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.63 |
Reflection shell | Resolution: 0.85→0.87 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.08 / Num. unique obs: 364 / CC1/2: 0.942 / % possible all: 56.4 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.85→22.46 Å / SU ML: 0.0543 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 8.1592 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 5.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→22.46 Å /
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Refine LS restraints |
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LS refinement shell |
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