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Open data
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Basic information
Entry | Database: PDB / ID: 1zdl | ||||||
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Title | Crystal Structure of Mouse Thioredoxin Reductase Type 2 | ||||||
![]() | Thioredoxin reductase 2, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / Selenocysteine / thioredoxin / reductase / flavoprotein | ||||||
Function / homology | ![]() response to oxygen radical / Detoxification of Reactive Oxygen Species / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / hemopoiesis / glutathione metabolic process / cell redox homeostasis / heart development / flavin adenine dinucleotide binding ...response to oxygen radical / Detoxification of Reactive Oxygen Species / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / hemopoiesis / glutathione metabolic process / cell redox homeostasis / heart development / flavin adenine dinucleotide binding / cellular response to oxidative stress / axon / neuronal cell body / dendrite / protein-containing complex binding / protein homodimerization activity / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Biterova, E.I. / Turanov, A.A. / Gladyshev, V.N. / Barycki, J.J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.2 KB | Display | ![]() |
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PDB format | ![]() | 83.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 945.5 KB | Display | ![]() |
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Full document | ![]() | 966.1 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zkqC ![]() 1h6vS 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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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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