+Open data
-Basic information
Entry | Database: PDB / ID: 1oes | ||||||
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Title | Oxidation state of protein tyrosine phosphatase 1B | ||||||
Components | PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 | ||||||
Keywords | HYDROLASE / PROTEIN TYROSINE PHOSPHATASE / OXIDATIVE REGULATION / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information 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 / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / 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 / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / positive regulation of protein tyrosine kinase activity / 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 / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / Growth hormone receptor signaling / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / negative regulation of MAP kinase activity / protein-tyrosine-phosphatase / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | van Montfort, R.L.M. / Congreve, M. / Tisi, D. / Carr, R. / Jhoti, H. | ||||||
Citation | Journal: Nature / Year: 2003 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: Journal: Science / Year: 1994 Title: Crystal Structure of Human Protein Tyrosine Phosphatase 1B Authors: Barford, D. / Flint, A.J. / Tonks, N.K. #2: Journal: Nature / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oes.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oes.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/1oes ftp://data.pdbj.org/pub/pdb/validation_reports/oe/1oes | HTTPS FTP |
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-Related structure data
Related structure data | 1oetC 1oeuC 1oevC 1c83S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37365.637 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-321 Source method: isolated from a genetically manipulated source Details: COVALENT BOND BETWEEN THE CATALYTIC CYS215 SG AND SER216 N RESULTING IN A NOVEL SULFENYLAMIDE SPECIES Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET19B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18031, protein-tyrosine-phosphatase | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | CATALYSES HYDROLYSISSequence details | TRUNCATED TO RESIDUES 1-321 CYS215 AND SER216 MODIFIED TO SULFENYLAM | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→76 Å / Num. obs: 23591 / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.8 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 83434 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C83 Resolution: 2.2→76.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.697 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SULFENYLAMIDE BOND BETWEEN THE CYS215 SG AND SER216 N ATOMS IS A NOVEL OXIDATION STATE OF PTP1B. IN ORDER TO DESCRIBE THIS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SULFENYLAMIDE BOND BETWEEN THE CYS215 SG AND SER216 N ATOMS IS A NOVEL OXIDATION STATE OF PTP1B. IN ORDER TO DESCRIBE THIS BONDING,CONECT AND LINK RECORDS HAVE BEEN ADDED BELOW.
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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: 34.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→76.7 Å
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