[English] 日本語
![](img/lk-miru.gif)
- PDB-8sfm: Crystal structure of the engineered SsoPox variant IVB10 in alter... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8sfm | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the engineered SsoPox variant IVB10 in alternate state | ||||||||||||||||||
![]() | Aryldialkylphosphatase | ||||||||||||||||||
![]() | HYDROLASE / Lactonase / quorum sensing / phosphotriesterase / arylesterase | ||||||||||||||||||
Function / homology | ![]() aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Jacquet, P. / Billot, R. / Shimon, A. / Hoekstra, N. / Bergonzi, C. / Jenks, A. / Daude, D. / Elias, M.H. | ||||||||||||||||||
Funding support | ![]() ![]()
| ||||||||||||||||||
![]() | ![]() Title: Changes in Active Site Loops Conformation Relates to a Transition from Lactonase to Phosphotriesterase Authors: Jacquet, P. / Billot, R. / Shimon, A. / Hoekstra, N. / Bergonzi, C. / Jenks, A. / Chabriere, E. / Daude, D. / Elias, M.H. | ||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 82.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 467.3 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sf2C ![]() 8sf9C ![]() 8sfaC ![]() 8sfbC ![]() 8sfcC ![]() 8sfdC ![]() 8sfkC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules D
#1: Protein | Mass: 35514.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: php, SSO2522 / Variant: IVB10 Production host: ![]() ![]() References: UniProt: Q97VT7, aryldialkylphosphatase |
---|
-Non-polymers , 6 types, 208 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-CO / | ||||||
#4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.42 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% (w/v) PEG 8000 and Tris-HCl buffer (pH 8.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.774901 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→68.85 Å / Num. obs: 101746 / % possible obs: 99.6 % / Redundancy: 3.72 % / CC1/2: 0.997 / Rrim(I) all: 0.069 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 3.77 % / Num. unique obs: 17921 / CC1/2: 0.874 / Rrim(I) all: 0.461 |
-
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: 1.5→39.72 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|