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- PDB-2hsh: Crystal structure of C73S mutant of human thioredoxin-1 oxidized ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hsh | ||||||
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Title | Crystal structure of C73S mutant of human thioredoxin-1 oxidized with H2O2 | ||||||
![]() | Thioredoxin | ||||||
![]() | OXIDOREDUCTASE / mutant | ||||||
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 / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / positive regulation of DNA binding / 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 / cytoplasm / cytosol 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 | ![]() | 64.8 KB | Display | ![]() |
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PDB format | ![]() | 48.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
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Full document | ![]() | 437.1 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hxkC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 11734.413 Da / Num. of mol.: 1 / Mutation: C73S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 50% MPD, 10 mM sodium acetate, 8% H2O2, pH 3.8, 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: Feb 12, 2005 / 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: 1.35→22.4 Å / Num. obs: 16046 / % possible obs: 86.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.9 / Num. unique all: 981 / % possible all: 50.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ERT Resolution: 1.35→22.37 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.78 / SU ML: 0.034 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.076 / ESU R Free: 0.064 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.477 Å2
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Refine analyze | Luzzati coordinate error obs: 0.143 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→22.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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