[English] 日本語
![](img/lk-miru.gif)
- PDB-7o0t: Crystal structure of Chloroflexus aggregans ene-reductase CaOYE h... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7o0t | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Chloroflexus aggregans ene-reductase CaOYE holoenzyme | ||||||
![]() | NADH:flavin oxidoreductase/NADH oxidase | ||||||
![]() | OXIDOREDUCTASE / ene-reductase / FMN-binding protein / Old Yellow Enzyme | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Robescu, M.S. / Niero, M. / Loprete, G. / Bergantino, E. / Cendron, L. | ||||||
![]() | ![]() Title: A New Thermophilic Ene-Reductase from the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aggregans . Authors: Robescu, M.S. / Niero, M. / Loprete, G. / Cendron, L. / Bergantino, E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 277.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 224.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 52.1 KB | Display | |
Data in CIF | ![]() | 71.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nuxS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37793.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: MD-66 / DSM 9485 / Gene: Cagg_2779 / Production host: ![]() ![]() #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-MLI / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.81 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM HEPES pH 7.0, 1.1 M sodium malonate dibasic monohydrate, 0.5% v/v Jeffamine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38.01 Å / Num. obs: 73908 / % possible obs: 99.3 % / Redundancy: 4.6 % / CC1/2: 0.969 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.4→2.61 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4571 / CC1/2: 0.74 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5nux Resolution: 2.4→38.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.95 Å2 / Biso mean: 34.188 Å2 / Biso min: 9.86 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→38.01 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|