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Yorodumi- PDB-3ean: Crystal structure of recombinant rat selenoprotein thioredoxin re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ean | ||||||
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Title | Crystal structure of recombinant rat selenoprotein thioredoxin reductase 1 with reduced C-terminal tail | ||||||
Components | Thioredoxin reductase 1 | ||||||
Keywords | OXIDOREDUCTASE / Selenoprotein / mammalian thioredoxin reductase 1 / selenocysteine / FAD / Flavoprotein / Redox-active center / NADP / Phosphoprotein / Selenium | ||||||
Function / homology | Function and homology information 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Sandalova, T. / Cheng, Q. / Lindqvist, Y. / Arner, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ean.cif.gz | 564.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ean.ent.gz | 465 KB | Display | PDB format |
PDBx/mmJSON format | 3ean.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ean_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 3ean_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 3ean_validation.xml.gz | 63.4 KB | Display | |
Data in CIF | 3ean_validation.cif.gz | 92.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/3ean ftp://data.pdbj.org/pub/pdb/validation_reports/ea/3ean | HTTPS FTP |
-Related structure data
Related structure data | 3eaoC 1h6vS 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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2 |
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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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-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.) Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley / Gene: Txnrd1, Trxr1 / Plasmid: pTRSter / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.16 % |
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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: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 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: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→84 Å / Num. all: 95938 / Num. obs: 95938 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 69 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.6 / Num. unique all: 13890 / Rsym value: 0.4 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H6V Resolution: 2.75→29.74 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 29.49 / SU ML: 0.27 / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.334 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→29.74 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: 2.75→2.821 Å / Total num. of bins used: 20
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