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Yorodumi- PDB-2x8g: Oxidized thioredoxin glutathione reductase from Schistosoma mansoni -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x8g | ||||||
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Title | Oxidized thioredoxin glutathione reductase from Schistosoma mansoni | ||||||
Components | THIOREDOXIN GLUTATHIONE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / REDOX-ACTIVE CENTER / DETOXIFICATION PATHWAY / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information 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 | SCHISTOSOMA MANSONI (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Angelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Mapping the Catalytic Cycle of Schistosoma Mansoni Thioredoxin Glutathione Reductase by X-Ray Crystallography Authors: Angelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A. #1: Journal: Proteins / Year: 2008 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. #2: Journal: J.Biol.Chem. / Year: 2009 Title: Inhibition of Schistosoma Mansoni Thioredoxin- Glutathione Reductase by Auranofin: Structural and Kinetic Aspects. Authors: Angelucci, F. / Sayed, A.A. / Williams, D.L. / Boumis, G. / Brunori, M. / Dimastrogiovanni, D. / Miele, A.E. / Pauly, F. / Bellelli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x8g.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x8g.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x8g_validation.pdf.gz | 729.6 KB | Display | wwPDB validaton report |
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Full document | 2x8g_full_validation.pdf.gz | 733.4 KB | Display | |
Data in XML | 2x8g_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 2x8g_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/2x8g ftp://data.pdbj.org/pub/pdb/validation_reports/x8/2x8g | HTTPS FTP |
-Related structure data
Related structure data | 2x8cC 2x8hC 2x99C 2v6oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65061.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q962Y6, EC: 1.6.4.5 |
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-Non-polymers , 5 types, 263 molecules
#2: Chemical | ChemComp-FAD / | ||||||
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#3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | RESIDUE 597 IS GIVEN AS X IN UNIPROT, IT IS CYS IN THIS CONSTRUCT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.062555 Å3/Da / Density % sol: 63 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.4 Details: VAPOR DIFFUSION, SITTING DROPS, CRYSTALS GROWN IN HEPES 0.1 M PH 7.4, PEG 3350 20%, KI 0.2M, 2-MERCAPTOETHANOL 5MM SOAKED WITH CUSO4 0.001 MM. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Type: BESSY / Wavelength: 0.918 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 52728 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.2 / % possible all: 92.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V6O Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.427 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5 OF CHAIN A ARE NOT VISIBLE BY THE ELECTRON DENSITY MAPS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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