[English] 日本語
![](img/lk-miru.gif)
- PDB-6sgn: Crystal structure of monooxygenase RutA complexed with 2,4-dimeth... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6sgn | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of monooxygenase RutA complexed with 2,4-dimethoxypyrimidine. | |||||||||
![]() | Pyrimidine monooxygenase RutA | |||||||||
![]() | FLAVOPROTEIN / monooxygenase / RutA / FMN / flavin-N5-oxide / bioengineering | |||||||||
Function / homology | ![]() pyrimidine oxygenase / uracil oxygenase activity / alkanesulfonate monooxygenase activity / thymine catabolic process / alkanesulfonate catabolic process / pyrimidine nucleobase catabolic process / uracil catabolic process / nitrogen utilization / monooxygenase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Saleem-Batcha, R. / Matthews, A. / Teufel, R. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Authors: Matthews, A. / Saleem-Batcha, R. / Sanders, J.N. / Stull, F. / Houk, K.N. / Teufel, R. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 84.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 930.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 936.9 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sggC ![]() 6sglC ![]() 6sgmC ![]() 6teeC ![]() 6tefC ![]() 6tegC ![]() 5wanS ![]() 6sgj C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39980.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: rutA, ycdM, b1012, JW0997 / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-LD8 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.03 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH 6.5, 1900 mM ammonium sulphate, 2-5% MPD (v/v), 1 mM 2,4-Dimethoxypyrimidine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.77 Å / Num. obs: 14850 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.998 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Num. unique obs: 2101 / CC1/2: 0.615 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5WAN Resolution: 2.501→43.606 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.359 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.289 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.701 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→43.606 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
|