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- PDB-7put: Crystal structure of Thioredoxin Reductase from Brugia Malayi in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7put | ||||||
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Title | Crystal structure of Thioredoxin Reductase from Brugia Malayi in complex with NADP(H) | ||||||
![]() | (Glutaredoxin domain-containing ...) x 2 | ||||||
![]() | FLAVOPROTEIN / Glutaredoxin / selenocysteine / OXIDOREDUCTASE | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fata, F. / Ardini, M. / Silvestri, I. / Gabriele, F. / Ippoliti, R. / Gencheva, R. / Cheng, Q. / Arner, E.S.J. / Angelucci, F. / Williams, D.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical and structural characterizations of thioredoxin reductase selenoproteins of the parasitic filarial nematodes Brugia malayi and Onchocerca volvulus. Authors: Fata, F. / Gencheva, R. / Cheng, Q. / Lullo, R. / Ardini, M. / Silvestri, I. / Gabriele, F. / Ippoliti, R. / Bulman, C.A. / Sakanari, J.A. / Williams, D.L. / Arner, E.S.J. / Angelucci, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 683.7 KB | Display | ![]() |
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PDB format | ![]() | 572.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 61.5 KB | Display | |
Data in CIF | ![]() | 82.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p0xC ![]() 7pvjC ![]() 4tr1S S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
-Glutaredoxin domain-containing ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 66118.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cysteine 345 of both chains A and B is modified into S-HYDROPEROXYCYSTEINE (PDB ID: 2CO) Source: (gene. exp.) ![]() Gene: bma-trxr-1, Bma-trxr-1, Bm2025, BM_Bm2025 Production host: ![]() Variant (production host): RF1-depleted / References: UniProt: A0A0J9XPH7 #2: Protein | | Mass: 66086.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: bma-trxr-1, Bma-trxr-1, Bm2025, BM_Bm2025 Production host: ![]() Variant (production host): RF1-depleted / References: UniProt: A0A0J9XPH7 |
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-Non-polymers , 4 types, 21 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ATR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ATR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-ATR / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.97 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris/HCl pH 8, 5mM DTT, 20% MPD / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.13 Å / Num. obs: 61904 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4537 / CC1/2: 0.874 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QFA_A, 4TR1 Resolution: 2.8→49.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 27.312 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.906 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 314.42 Å2 / Biso mean: 103.503 Å2 / Biso min: 47.98 Å2
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Refinement step | Cycle: final / Resolution: 2.8→49.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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