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- PDB-2v6o: Structure of Schistosoma mansoni Thioredoxin-Glutathione Reductas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v6o | ||||||
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Title | Structure of Schistosoma mansoni Thioredoxin-Glutathione Reductase (SmTGR) | ||||||
![]() | THIOREDOXIN GLUTATHIONE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / FAD / FLAVOPROTEIN / CHIMERIC ENZYME / THIOL-MEDIATED DETOXIFICATION PATHWAY / REDOX-ACTIVE CENTER | ||||||
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 / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miele, A.E. / Angelucci, F. / Boumis, G. / Dimastrogiovanni, D. / Bellelli, A. / Brunori, M. | ||||||
![]() | ![]() Title: Glutathione Reductase and Thioredoxin Reductase at the Crossroad: The Structure of Schistosoma Mansoni Thioredoxin Glutathione Reductase Authors: Angelucci, F. / Miele, A.E. / Boumis, G. / Dimastrogiovanni, D. / Brunori, M. / Bellelli, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.3 KB | Display | ![]() |
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PDB format | ![]() | 103.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.9 KB | Display | ![]() |
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Full document | ![]() | 731.7 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h6vS S: Starting model for refinement |
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Similar structure data |
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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
#1: Protein | Mass: 64900.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-596 Source method: isolated from a genetically manipulated source Details: FAD COFACTOR BOUND / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-FAD / | ||||||||
#3: Chemical | ChemComp-PG4 / #4: Chemical | ChemComp-NO3 / | #5: Water | ChemComp-HOH / | Compound details | BELONGS TO THE CLASS-I PYRIDINE NUCLEOTIDE | Sequence details | 2 RESIDUES DELETION 597-598 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.6 % Description: AFTER FIXING THE FIRST DOMAIN, THE SECOND DOMAIN WAS SEARCHED USING 1Z7R AS STARTING MODEL. |
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Crystal grow | pH: 7.2 Details: 22% PEG 3350, 0.1M HEPES PH 7.2, 0.2M NANO3, 5MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 39579 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.2 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H6V Resolution: 2.2→19.92 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.339 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY FOR RESIDUES 1-7 AND 594-597 WAS NOT VISIBLE, THEREFORE THESE AMINO ACIDS WERE NOT MODELED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.92 Å
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Refine LS restraints |
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