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- PDB-7pvj: 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: 7pvj | ||||||
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Title | Crystal structure of Thioredoxin Reductase from Brugia Malayi in complex with auranofin | ||||||
![]() | Glutaredoxin domain-containing protein | ||||||
![]() | 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 | ![]() | 685.2 KB | Display | ![]() |
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PDB format | ![]() | 576 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 | ![]() | 60.8 KB | Display | |
Data in CIF | ![]() | 81.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p0xC ![]() 7putC ![]() 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 66086.781 Da / Num. of mol.: 3 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 , 5 types, 11 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/ATR.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/AU.gif)
![](data/chem/img/ATR.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/AU.gif)
#2: Chemical | #3: Chemical | ChemComp-ATR / | #4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-AU / | |
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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: 3.03 Å3/Da / Density % sol: 59.47 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 14% MPD, 0.1 M Tris/HCl pH 7.5, 5mM DTT / PH range: 7.5-8.2 |
-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: Jul 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→49.31 Å / Num. obs: 46008 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4474 / CC1/2: 0.904 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QFA_A; 4TR1 Resolution: 3.1→49.36 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 39.604 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.4 / 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: 357.25 Å2 / Biso mean: 117.47 Å2 / Biso min: 55.93 Å2
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Refinement step | Cycle: final / Resolution: 3.1→49.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 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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