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- PDB-8cci: Crystal structure of Mycobacterium smegmatis thioredoxin reductase -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cci | ||||||
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Title | Crystal structure of Mycobacterium smegmatis thioredoxin reductase | ||||||
![]() | 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 | ![]()
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![]() | ![]() Title: Novel starting points for fragment-based drug design against mycobacterial thioredoxin reductase identified using crystallographic fragment screening. Authors: Fusser, F.T. / Wollenhaupt, J. / Weiss, M.S. / Kummel, D. / Koch, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.1 KB | Display | ![]() |
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PDB format | ![]() | 105.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 731.2 KB | Display | ![]() |
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Full document | ![]() | 737 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uthS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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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: ![]() ![]() |
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-Non-polymers , 5 types, 175 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.66 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 2.16 M Sodium malonate dibasic monohydrate, 10% glycerol , soaked with 5% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→46.81 Å / Num. obs: 59648 / % possible obs: 99.72 % / Redundancy: 9.8 % / Biso Wilson estimate: 24.09 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.01 |
Reflection shell | Resolution: 1.56→1.616 Å / Mean I/σ(I) obs: 0.51 / Num. unique obs: 5883 / CC1/2: 0.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UTH Resolution: 1.56→46.81 Å / SU ML: 0.2929 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.787 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→46.81 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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