[English] 日本語
![](img/lk-miru.gif)
- PDB-8ccj: Crystal structure of Mycobacterium smegmatis thioredoxin reductas... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8ccj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with NADPH | ||||||
![]() | Thioredoxin reductase | ||||||
![]() | OXIDOREDUCTASE / TrxR | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fuesser, F.T. / Koch, O. / Kuemmel, D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Fragment-based design of mycobacterial thioredoxin reductase inhibitors based on computational exploration of a huge virtual space Authors: Fuesser, F.T. / Otten, P. / Kuemmel, D. / Junker, A. / Koch, O. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 168 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 107.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1010.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1015.9 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cckC ![]() 8cclC ![]() 8ccmC ![]() 8cciS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34578.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: trxB / Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 198 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-NAP / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.79 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: Sodium malonate dibasic monohydrate 2.16 M, Glycerol 10%, pH7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 4, 2022 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.1 Å / Num. obs: 39176 / % possible obs: 99.61 % / Redundancy: 19.9 % / Biso Wilson estimate: 27.83 Å2 / CC1/2: 1 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.8→1.864 Å / Mean I/σ(I) obs: 2.51 / Num. unique obs: 3788 / CC1/2: 0.93 / % possible all: 98.53 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8CCI Resolution: 1.8→31.1 Å / SU ML: 0.2007 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.27 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→31.1 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|