+Open data
-Basic information
Entry | Database: PDB / ID: 8vpj | ||||||
---|---|---|---|---|---|---|---|
Title | UIC-11-BPE extension of UIC-1 | ||||||
Components | UIC-11-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: 1.5 Å | ||||||
Authors | Ganatra, P. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vpj.cif.gz | 19.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vpj.ent.gz | 11.8 KB | Display | PDB format |
PDBx/mmJSON format | 8vpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vpj_validation.pdf.gz | 408.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8vpj_full_validation.pdf.gz | 408.4 KB | Display | |
Data in XML | 8vpj_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 8vpj_validation.cif.gz | 2.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/8vpj ftp://data.pdbj.org/pub/pdb/validation_reports/vp/8vpj | HTTPS FTP |
-Related structure data
Related structure data | 8vogC 8vp7C 8vpcC 8vpdC 8vpeC 8vpsC 8vptC 8vpxC 8vpyC 8vpzC 8vq0C 8vsfC 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 on special symmetry positions |
|
-Components
#1: Protein/peptide | Mass: 1530.772 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: 3.27 Å3/Da / Density % sol: 62.4 % |
---|---|
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: 0.6199 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6199 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→24.3 Å / Num. obs: 2458 / % possible obs: 97.89 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.36 Å2 / CC1/2: 1 / Net I/σ(I): 16.44 |
Reflection shell | Resolution: 1.5→1.554 Å / Num. unique obs: 234 / CC1/2: 0.925 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.3 Å / SU ML: 0.1615 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 39.9381 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: 42.76 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→24.3 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|