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- PDB-3eao: Crystal structure of recombinant rat selenoprotein thioredoxin re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eao | ||||||
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Title | Crystal structure of recombinant rat selenoprotein thioredoxin reductase 1 with oxidized C-terminal tail | ||||||
![]() | Thioredoxin reductase 1, cytoplasmic | ||||||
![]() | OXIDOREDUCTASE / Selenoprotein / mammalian thioredoxin reductase 1 / selenocysteine / selenenylsulfide / FAD / Flavoprotein / NADP / Phosphoprotein / Redox-active center / Selenium | ||||||
Function / homology | ![]() selenate reductase activity / halogen metabolic process / Metabolism of ingested MeSeO2H into MeSeH / benzene-containing compound metabolic process / Interconversion of nucleotide di- and triphosphates / Detoxification of Reactive Oxygen Species / NADPH peroxidase / NADPH peroxidase activity / cellular response to hyperoxia / TP53 Regulates Metabolic Genes ...selenate reductase activity / halogen metabolic process / Metabolism of ingested MeSeO2H into MeSeH / benzene-containing compound metabolic process / Interconversion of nucleotide di- and triphosphates / Detoxification of Reactive Oxygen Species / NADPH peroxidase / NADPH peroxidase activity / cellular response to hyperoxia / TP53 Regulates Metabolic Genes / NADPH oxidation / mercury ion binding / NAD(P)H oxidase H2O2-forming activity / selenocysteine metabolic process / thioredoxin-disulfide reductase / response to selenium ion / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / mesoderm formation / response to axon injury / response to hyperoxia / gastrulation / cellular response to copper ion / FAD binding / glutathione metabolic process / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to oxidative stress / response to oxidative stress / cell population proliferation / response to xenobiotic stimulus / positive regulation of apoptotic process / neuronal cell body / mitochondrion / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sandalova, T. / Cheng, Q. / Lindqvist, Y. / Arner, E. | ||||||
![]() | ![]() Title: Crystal structure and catalysis of the selenoprotein thioredoxin reductase 1. Authors: Cheng, Q. / Sandalova, T. / Lindqvist, Y. / Arner, E.S. #1: Journal: J.Mol.Biol. / Year: 1999 Title: High-level expression in Escherichia coli of selenocysteine-containing rat thioredoxin reductase utilizing gene fusions with engineered bacterial-type SECIS elements and co-expression with the ...Title: High-level expression in Escherichia coli of selenocysteine-containing rat thioredoxin reductase utilizing gene fusions with engineered bacterial-type SECIS elements and co-expression with the selA, selB and selC genes. Authors: Arner, E.S. / Sarioglu, H. / Lottspeich, F. / Holmgren, A. / Bock, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 563.2 KB | Display | ![]() |
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PDB format | ![]() | 463.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 109 KB | Display | |
Data in CIF | ![]() | 141.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eanSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Details | The biological assembly is a dimer, the unit cell contains three dimers |
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Components
#1: Protein | Mass: 54736.293 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: residue 426 is Ile / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O89049, thioredoxin-disulfide reductase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-NAP / #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE MATCHES WITH NP_113802 FROM NCBI DATABASE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, PEG 3350 15%, 12% of ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2007 / Details: mirrors |
Radiation | Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→64 Å / Num. all: 64804 / Num. obs: 64804 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 3.101→3.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3EAN Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.83 / SU B: 26.935 / SU ML: 0.46 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 56.314 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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