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Open data
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Basic information
Entry | Database: PDB / ID: 4oo4 | ||||||
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Title | Crystal Structure of Human Thioredoxin Mutant | ||||||
![]() | Thioredoxin | ||||||
![]() | OXIDOREDUCTASE / S-nitrosation | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | The, J. / Weichsel, A. / Montfort, W.R. | ||||||
![]() | ![]() Title: Crystal Structure of a Thioredoxin Mutant Displays a Dynamic N-terminal Loop Surrounding an S-nitrosation Site Authors: The, J. / Weichsel, A. / Montfort, W.R. #1: ![]() Title: Crystal structure of human thioredoxin revealing an unraveled helix and exposed S-nitrosation site. Authors: Weichsel, A. / Kem, M. / 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 | ![]() | 135.7 KB | Display | ![]() |
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PDB format | ![]() | 109.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.5 KB | Display | ![]() |
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Full document | ![]() | 438.3 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oo5C ![]() 1ertS C: citing same article ( S: Starting model for refinement |
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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: 11661.297 Da / Num. of mol.: 2 / Mutation: Q63A, C69S, C73S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.36 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% PEG 3350, 0.1 M sodium acetate, 2 mM DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2011 / Details: RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→50.94 Å / Num. all: 88291 / Num. obs: 88291 / % possible obs: 84.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 0.97→1.02 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.6 / % possible all: 44.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ERT Resolution: 0.97→35.75 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.991 / SU ML: 0.024 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.371 Å2
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Refine analyze | Luzzati coordinate error obs: 0.133 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→35.75 Å
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Refine LS restraints |
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