[English] 日本語
![](img/lk-miru.gif)
- PDB-6xxz: Crystal structure of a de novo designed parallel four-helix coile... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6xxz | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a de novo designed parallel four-helix coiled coil, 2-EK-4 | ||||||||||||
![]() | 2-EK-4 | ||||||||||||
![]() | DE NOVO PROTEIN / coiled coil / tetramer / parallel | ||||||||||||
Function / homology | PROPANOIC ACID![]() | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Edgell, C.L. / Savery, N.J. / Woolfson, D.N. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: RobustDe Novo-Designed Homotetrameric Coiled Coils. Authors: Edgell, C.L. / Savery, N.J. / Woolfson, D.N. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 42.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 27.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein/peptide | Mass: 3462.024 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.87 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M sodium propionate, 0.1 M sodium cacodylate trihydrate, 0.1 M bis-tris propane, 25% PEG1500, pH 7.0, supplemented with 25% glycerol for cryo-protection |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.94 Å / Num. obs: 6093 / % possible obs: 99.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 19.73 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 308 / CC1/2: 0.978 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.34 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→43.94 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -15.0354676102 Å / Origin y: -8.20651094721 Å / Origin z: 13.7493872719 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |