+Open data
-Basic information
Entry | Database: PDB / ID: 8vsf | ||||||
---|---|---|---|---|---|---|---|
Title | UIC-13-BPE extension of UIC-1 | ||||||
Components | UIC-13-BPE | ||||||
Keywords | DE NOVO PROTEIN / synthetic construct | ||||||
Function / homology | ACETONITRILE Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å | ||||||
Authors | Ganatra, P. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2024 Title: Diverse Proteomimetic Frameworks via Rational Design of pi-Stacking Peptide Tectons. Authors: Ganatra, P. / Wang, D.F. / Ganatra, V. / Dang, V.T. / Nguyen, A.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vsf.cif.gz | 21 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vsf.ent.gz | 13.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vsf_validation.pdf.gz | 370.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8vsf_full_validation.pdf.gz | 370.7 KB | Display | |
Data in XML | 8vsf_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 8vsf_validation.cif.gz | 2.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/8vsf ftp://data.pdbj.org/pub/pdb/validation_reports/vs/8vsf | HTTPS FTP |
-Related structure data
Related structure data | 8vogC 8vp7C 8vpcC 8vpdC 8vpeC 8vpjC 8vpsC 8vptC 8vpxC 8vpyC 8vpzC 8vq0C 8vt8C 8vw7C 8vw8C 8vxsC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 1686.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: Chemical | ChemComp-CCN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.92 % |
---|---|
Crystal grow | Temperature: 298 K / Method: slow cooling / Details: Acetonitrile, water |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.61992 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.61992 Å / Relative weight: 1 |
Reflection | Resolution: 1.11→16.69 Å / Num. obs: 7064 / % possible obs: 99.32 % / Redundancy: 24.4 % / Biso Wilson estimate: 15.07 Å2 / CC1/2: 1 / Net I/σ(I): 16.54 |
Reflection shell | Resolution: 1.11→1.15 Å / Num. unique obs: 679 / CC1/2: 0.736 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.11→16.69 Å / SU ML: 0.1751 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.0699 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.11→16.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|