+Open data
-Basic information
Entry | Database: PDB / ID: 8vpy | ||||||
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Title | UIC-16-MER extension of UIC-1 | ||||||
Components | UIC-16-MER | ||||||
Keywords | DE NOVO PROTEIN / synthetic construct | ||||||
Function / homology | METHANOL Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Ganatra, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Diverse Proteomimetic Frameworks via Rational Design of pi-Stacking Peptide Tectons Authors: Ganatra, P. / Wang, D.F. / Ren, Z. / Dang, V.T. / Nguyen, A.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vpy.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vpy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vpy_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 8vpy_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 8vpy_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 8vpy_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/8vpy ftp://data.pdbj.org/pub/pdb/validation_reports/vp/8vpy | HTTPS FTP |
-Related structure data
Related structure data | 8vogC 8vp7C 8vpcC 8vpdC 8vpeC 8vpjC 8vpsC 8vptC 8vpxC 8vpzC 8vq0C 8vsfC 8vt8C 8vw7C 8vw8C 8vxsC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1969.336 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MOH / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.57 % |
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Crystal grow | Temperature: 298 K / Method: slow cooling / Details: methanol and water |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.729317 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.729317 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→21.01 Å / Num. obs: 16793 / % possible obs: 96.31 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.75 Å2 / CC1/2: 0.996 / Net I/σ(I): 5.63 |
Reflection shell | Resolution: 1.21→1.253 Å / Num. unique obs: 1682 / CC1/2: 0.474 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→21.01 Å / SU ML: 0.2102 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.1842 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: 18.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.21→21.01 Å
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Refine LS restraints |
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LS refinement shell |
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