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Open data
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Basic information
Entry | Database: PDB / ID: 1oeu | ||||||
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Title | Oxidation state of protein tyrosine phosphatase 1B | ||||||
![]() | PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 | ||||||
![]() | HYDROLASE / PROTEIN TYROSINE PHOSPHATASE / OXIDATIVE REGULATION / PHOSPHORYLATION | ||||||
Function / homology | ![]() regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | van Montfort, R.L.M. / Congreve, M. / Tisi, D. / Carr, R. / Jhoti, H. | ||||||
![]() | ![]() Title: Oxidation state of the active-site cysteine in protein tyrosine phosphatase 1B. Authors: van Montfort, R.L. / Congreve, M. / Tisi, D. / Carr, R. / Jhoti, H. #1: ![]() Title: Crystal Structure of Human Protein Tyrosine Phosphatase 1B Authors: Barford, D. / Flint, A.J. / Tonks, N.K. #2: ![]() Title: Redox Regulation of Protein Tyrosine Phosphatase Involves a Sulfenyl-Amide Intermediate Authors: Salmeen, A. / Andersen, J.N. / Myers, M.P. / Meng, T.-C. / Hinks, J.A. / Tonks, N.K. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.1 KB | Display | ![]() |
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PDB format | ![]() | 56.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 368.8 KB | Display | ![]() |
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Full document | ![]() | 373 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oesC ![]() 1oetC ![]() 1oevC ![]() 1c83S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37397.637 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-321 Source method: isolated from a genetically manipulated source Details: THE CATALYTIC CYS215 IS MODIFIED TO SULFINIC ACID (CYS-SO2H) Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | CATALYSES HYDROLYSISSequence details | TRUNCATED TO RESIDUES 1-321 CYS215 MODIFIED TO CYS-SO2H | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.8 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 12-18% PEG4000, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM ACETATE, 10MM DTT | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Barford, D., (1994) J. Mol. Biol., 239, 726. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Details: CONFOCAL MULTILAYER OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→76 Å / Num. obs: 16237 / % possible obs: 95.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. measured all: 29624 / Rmerge(I) obs: 0.172 |
Reflection shell | *PLUS % possible obs: 95.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1C83 Resolution: 2.5→76.7 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.842 / SU B: 11.14 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.MODIFICATION OF CYS215 TO SULFINIC ACID
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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: 22.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→76.7 Å
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