[English] 日本語
![](img/lk-miru.gif)
- PDB-8gk1: Porous framework formed by assembly of a bipyridyl-conjugated hel... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8gk1 | ||||||
---|---|---|---|---|---|---|---|
Title | Porous framework formed by assembly of a bipyridyl-conjugated helical peptide | ||||||
![]() | LEU-AIB-ALA-AIB-LEU-AIB-GLN-AIB-LEU | ||||||
![]() | DE NOVO PROTEIN | ||||||
Function / homology | ACETONITRILE / Chem-I77 / NICOTINIC ACID![]() | ||||||
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 | ![]() | 19.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 10.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 613.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 613.5 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 3.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gb9C ![]() 8gbaC ![]() 8gbhC ![]() 8gbiC ![]() 8gbmC ![]() 8gboC ![]() 8gd6C ![]() 8gd8C ![]() 8givC ![]() 8gj7C ![]() 8gk2C ![]() 8gk9C ![]() 8gkbC ![]() 8gkxC ![]() 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: 897.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: Chemical | ChemComp-NIO / |
#3: Chemical | ChemComp-I77 / |
#4: Chemical | ChemComp-CCN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.91 % |
---|---|
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 4, 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: 0.83→27.8 Å / Num. obs: 13216 / % possible obs: 86.79 % / Redundancy: 12.2 % / Biso Wilson estimate: 2.71 Å2 / Rmerge(I) obs: 0.285 / Net I/σ(I): 16.03 |
Reflection shell | Resolution: 0.83→0.8597 Å / Rmerge(I) obs: 0.8457 / Num. unique obs: 359 |
-
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: 5.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.83→27.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|