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Open data
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Basic information
Entry | Database: PDB / ID: 2hxk | ||||||
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Title | Crystal structure of S-nitroso thioredoxin | ||||||
![]() | Thioredoxin | ||||||
![]() | OXIDOREDUCTASE / S-nitrosation / S-nitrosocysteine | ||||||
Function / homology | ![]() Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide ...Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / positive regulation of DNA binding / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Weichsel, A. / Montfort, W.R. | ||||||
![]() | ![]() Title: Buried s-nitrosocysteine revealed in crystal structures of human thioredoxin. Authors: Weichsel, A. / Brailey, J.L. / Montfort, W.R. #1: ![]() Title: Crystal structures of reduced, oxidized, and mutated human thioredoxins: evidence for a regulatory homodimer Authors: Weichsel, A. / Gasdaska, J.R. / Powis, G. / Montfort, W.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.5 KB | Display | ![]() |
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PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2hshC ![]() 2ifqC ![]() 2iiyC ![]() 1ertS 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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Components
#1: Protein | Mass: 11808.474 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 25.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 32% PEG 1500, 50 mM sodium phosphate, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 8, 2006 / Details: osmic mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→24.2 Å / Num. all: 29229 / Num. obs: 29229 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3122 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ERT Resolution: 1.65→24.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.223 / SU ML: 0.079 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.127 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.156 Å2
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Refine analyze | Luzzati coordinate error obs: 0.189 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→24.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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