[English] 日本語
![](img/lk-miru.gif)
- PDB-8gkx: Porous framework formed by assembly of a bipyridyl-conjugated hel... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8gkx | ||||||
---|---|---|---|---|---|---|---|
Title | Porous framework formed by assembly of a bipyridyl-conjugated helical peptide | ||||||
![]() | LEU-AIB-ALA-AIB-LEU-HIS-GLN-AIB-LEU | ||||||
![]() | DE NOVO PROTEIN | ||||||
Function / homology | ethyl 5'-formyl[2,2'-bipyridine]-5-carboxylate / Chem-I77![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hess, S.S. / Nguyen, A.I. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks. Authors: Hess, S.S. / Coppola, F. / Dang, V.T. / Tran, P.N. / Mickel, P.J. / Oktawiec, J. / Ren, Z. / Kral, P. / Nguyen, A.I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 30.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 18.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8gb9C ![]() 8gbaC ![]() 8gbhC ![]() 8gbiC ![]() 8gbmC ![]() 8gboC ![]() 8gd6C ![]() 8gd8C ![]() 8givC ![]() 8gj7C ![]() 8gk1C ![]() 8gk2C ![]() 8gk9C ![]() 8gkbC ![]() 8gl0C ![]() 8gl4C ![]() 8gl5C ![]() 8sw2C ![]() 8sy4C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 950.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
---|---|
Crystal grow | Temperature: 298 K / Method: slow cooling / Details: Water/Acetonitrile |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6888 Å / Relative weight: 1 |
Reflection | Resolution: 0.81→17.93 Å / Num. obs: 32406 / % possible obs: 97.34 % / Redundancy: 6.1 % / Biso Wilson estimate: 4 Å2 / Rmerge(I) obs: 0.1108 / Net I/σ(I): 11.26 |
Reflection shell | Resolution: 0.81→0.839 Å / Rmerge(I) obs: 0.557 / Num. unique obs: 1718 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 5.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.81→17.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|