[English] 日本語
![](img/lk-miru.gif)
- PDB-8uqy: Round 18 Arylesterase Variant of Phosphotriesterase Bound to Euro... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8uqy | ||||||
---|---|---|---|---|---|---|---|
Title | Round 18 Arylesterase Variant of Phosphotriesterase Bound to Europium(III) Measured at 9.5 keV | ||||||
![]() | Phosphotriesterase variant PTE-R18 | ||||||
![]() | HYDROLASE / Phosphotriesterase / 9.5 keV / Europium | ||||||
Function / homology | ![]() catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Breeze, C.W. / Frkic, R.L. / Campbell, E.C. / Jackson, C.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase. Authors: Breeze, C.W. / Nakano, Y. / Campbell, E.C. / Frkic, R.L. / Lupton, D.W. / Jackson, C.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 378.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 314.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 845.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 849.6 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uqwC ![]() 8uqxC ![]() 8uqzC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 36208.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-EU3 / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.7 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Sodium cacodylate, 14% (v/v) MPD, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.305 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→44.67 Å / Num. obs: 63759 / % possible obs: 100 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.022 / Rrim(I) all: 0.111 / Χ2: 1.02 / Net I/σ(I): 18.7 / Num. measured all: 1673385 |
Reflection shell | Resolution: 1.78→1.82 Å / % possible obs: 100 % / Redundancy: 22.2 % / Rmerge(I) obs: 3.131 / Num. measured all: 79796 / Num. unique obs: 3593 / CC1/2: 0.655 / Rpim(I) all: 0.668 / Rrim(I) all: 3.204 / Χ2: 1.01 / Net I/σ(I) obs: 1.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→42.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 15.4909 Å / Origin y: 22.8051 Å / Origin z: 22.0714 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |