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Yorodumi- PDB-2x8c: Thioredoxin glutathione reductase from Schistosoma mansoni with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x8c | ||||||
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Title | Thioredoxin glutathione reductase from Schistosoma mansoni with the reduced C-terminal end | ||||||
Components | THIOREDOXIN GLUTATHIONE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE/FLAVOPROTEIN / OXIDOREDUCTASE-FLAVOPROTEIN COMPLEX / DETOXIFICATION PATHWAY | ||||||
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: 3.1 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 | 2x8c.cif.gz | 233.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x8c.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 2x8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x8c_validation.pdf.gz | 925.6 KB | Display | wwPDB validaton report |
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Full document | 2x8c_full_validation.pdf.gz | 944.7 KB | Display | |
Data in XML | 2x8c_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 2x8c_validation.cif.gz | 57.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/2x8c ftp://data.pdbj.org/pub/pdb/validation_reports/x8/2x8c | HTTPS FTP |
-Related structure data
Related structure data | 2x8gC 2x8hC 2x99C 2v6oS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 65061.145 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | 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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: VAPOR DIFFUSION, SITTING DROP, 0.2 M MG-FORMATE, 20% PEG 6000, 0.1 M SODIUM HEPES, PH 7.0-7.5, TEMP 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 24223 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 63.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V6O Resolution: 3.1→92.76 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.828 / SU B: 23.351 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R Free: 0.569 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5 AND 594-598 OF CHAIN A AND RESIDUES 1-5 OF CHAIN B ARE NOT VISIBLE BY THE 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: 43.488 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→92.76 Å
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Refine LS restraints |
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