[English] 日本語
![](img/lk-miru.gif)
- PDB-7ov7: The hybrid cage formed between Pizza6-S and Cu(II)-substituted tr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ov7 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The hybrid cage formed between Pizza6-S and Cu(II)-substituted trilacunary Keggin | |||||||||||||||
![]() | Pizza6-S | |||||||||||||||
![]() | BIOSYNTHETIC PROTEIN / Designer protein / protein design / POM / Polyoxometalate / hybrid / cage / Cu / Keggin | |||||||||||||||
Function / homology | COPPER (II) ION / : / Trilacunary Keggin![]() | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Vandebroek, L. / Noguchi, H. / Anyushin, A. / Van Meervelt, L. / Voet, A.R.D. / Parac-Vogt, T.N. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Hierarchical Self-Assembly of a Supramolecular Protein-Metal Cage Encapsulating a Polyoxometalate Guest Authors: Vandebroek, L. / Noguchi, H. / Anyushin, A. / Van Meervelt, L. / Voet, A.R.D. / Parac-Vogt, T.N. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 111.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3ww9S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 25719.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.94 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES, 25% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.213 Å / Num. obs: 69759 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.998 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2151 / CC1/2: 0.888 / Rpim(I) all: 0.262 / Rrim(I) all: 0.823 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3WW9 Resolution: 1.8→49.213 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.69 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.02 Å2 / Biso mean: 30.8563 Å2 / Biso min: 12.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→49.213 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|