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Open data
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Basic information
Entry | Database: PDB / ID: 4oo5 | ||||||
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Title | Crystal Structure of S-nitrosated Human Thioredoxin Mutant | ||||||
![]() | 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 / 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 | ![]() | 38.6 KB | Display | ![]() |
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PDB format | ![]() | 26.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421 KB | Display | ![]() |
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Full document | ![]() | 422.5 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oo4C ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 11747.345 Da / Num. of mol.: 1 / Mutation: C69S, C73S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.93 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 21% PEG 3350, 0.1 M sodium acetate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 2012 / 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: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→25.45 Å / Num. all: 12978 / Num. obs: 12978 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.54→1.63 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1837 / % possible all: 95.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ERT Resolution: 1.54→25.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.969 / SU ML: 0.101 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.114 / 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: 29.765 Å2
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Refine analyze | Luzzati coordinate error obs: 0.209 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→25.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.544→1.584 Å / Total num. of bins used: 20
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