+Open data
-Basic information
Entry | Database: PDB / ID: 1zdl | ||||||
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Title | Crystal Structure of Mouse Thioredoxin Reductase Type 2 | ||||||
Components | Thioredoxin reductase 2, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Selenocysteine / thioredoxin / reductase / flavoprotein | ||||||
Function / homology | Function and homology information response to oxygen radical / Detoxification of Reactive Oxygen Species / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / hemopoiesis / cell redox homeostasis / flavin adenine dinucleotide binding / heart development / axon / dendrite ...response to oxygen radical / Detoxification of Reactive Oxygen Species / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / hemopoiesis / cell redox homeostasis / flavin adenine dinucleotide binding / heart development / axon / dendrite / neuronal cell body / protein-containing complex binding / protein homodimerization activity / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Biterova, E.I. / Turanov, A.A. / Gladyshev, V.N. / Barycki, J.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Crystal structures of oxidized and reduced mitochondrial thioredoxin reductase provide molecular details of the reaction mechanism. Authors: Biterova, E.I. / Turanov, A.A. / Gladyshev, V.N. / Barycki, J.J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Three-dimensional structure of a mammalian thioredoxin reductase: Implications for mechanism and evolution of a selenocysteine-dependent enzyme. Authors: Sandalova, T. / Zhong, L. / Lindqvist, Y. / Holmgren, A. / Schneider, G. #2: Journal: J.Mol.Biol. / Year: 1987 Title: Refined structure of glutathione reductase at 1.54 A resolution. Authors: Karplus, P.A. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zdl.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zdl.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zdl ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zdl | HTTPS FTP |
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-Related structure data
Related structure data | 1zkqC 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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Unit cell |
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-Components
#1: Protein | Mass: 55816.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Txnrd2, Trxr2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: Q9JLT4, thioredoxin-disulfide reductase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM MES, 24% Peg 550 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→32.68 Å / Num. all: 12754 / Num. obs: 12754 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.29 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 16.66 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 6.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1H6V Resolution: 3→32.69 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 182218.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10.2389 Å2 / ksol: 0.289304 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→32.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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