+Open data
-Basic information
Entry | Database: PDB / ID: 1zkq | ||||||
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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 / heart development / flavin adenine dinucleotide binding / axon / neuronal cell body ...response to oxygen radical / Detoxification of Reactive Oxygen Species / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / hemopoiesis / cell redox homeostasis / heart development / flavin adenine dinucleotide binding / axon / neuronal cell body / dendrite / 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: 2.6 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 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 | 1zkq.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zkq.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/1zkq ftp://data.pdbj.org/pub/pdb/validation_reports/zk/1zkq | HTTPS FTP |
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-Related structure data
Related structure data | 1zdlC 1h6vS 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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Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit. |
-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: 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: 2.7 Å3/Da / Density % sol: 54 % |
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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 18, 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: 2.6→37.3 Å / Num. all: 19370 / Num. obs: 19370 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.88 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 15.99 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 6.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1H6V Resolution: 2.6→37.4 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 224842.22 / 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: 36.3488 Å2 / ksol: 0.325839 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→37.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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