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- PDB-1oem: PTP1B with the catalytic cysteine oxidized to a sulfenyl-amide bond -

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Basic information

Entry
Database: PDB / ID: 1oem
TitlePTP1B with the catalytic cysteine oxidized to a sulfenyl-amide bond
ComponentsPROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1
KeywordsHYDROLASE / PHOSPHORYLATION / PHOSPHATASE
Function / homology
Function and homology information


PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / negative regulation of PERK-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of MAP kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / positive regulation of systemic arterial blood pressure / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNA/IFNB signaling / cellular response to angiotensin / regulation of proteolysis / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of cell-substrate adhesion / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / cellular response to unfolded protein / regulation of signal transduction / Growth hormone receptor signaling / Regulation of IFNG signaling / negative regulation of signal transduction / positive regulation of cardiac muscle cell apoptotic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of heart rate / endoplasmic reticulum unfolded protein response / ephrin receptor binding / MECP2 regulates neuronal receptors and channels / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / cellular response to fibroblast growth factor stimulus / phosphoprotein phosphatase activity / Integrin signaling / protein-tyrosine-phosphatase / cellular response to nitric oxide / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / insulin receptor binding / response to nutrient levels / cellular response to nerve growth factor stimulus / Negative regulation of MET activity / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / positive regulation of JNK cascade / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / cadherin binding / mitochondrial matrix / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSalmeen, A. / Andersen, J.N. / Myers, M.P. / Meng, T.C. / Hinks, J.A. / Tonks, N.K. / Barford, D.
CitationJournal: 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
DepositionMar 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1


Theoretical massNumber of molelcules
Total (without water)37,3661
Polymers37,3661
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.218, 88.218, 103.787
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 / PROTEIN-TYROSINE PHOSPHATASE 1B / PTP-1B


Mass: 37365.637 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-321
Source method: isolated from a genetically manipulated source
Details: SULFENYL-AMIDE BOND BETWEEN CYS215 SG AND SER216 N / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES THE HYDROLYSIS OF PROTEIN TYROSINE PHOSPHATE TO PROTEIN TYROSINE AND PHOSPHATE.BELONGS TO ...CATALYSES THE HYDROLYSIS OF PROTEIN TYROSINE PHOSPHATE TO PROTEIN TYROSINE AND PHOSPHATE.BELONGS TO THE NON-RECEPTOR CLASS OF THE PROTEIN-TYROSINE PHOSPHATASE FAMILY.
Sequence detailsMODRES: 1OEM CYS X 215() MODIFIED CYSTEINE, OXIDATION TO A SULFENYL AMIDE BOND BETWEEN CYS 215, SER ...MODRES: 1OEM CYS X 215() MODIFIED CYSTEINE, OXIDATION TO A SULFENYL AMIDE BOND BETWEEN CYS 215, SER 216 MODRES: 1OEM SER X 216() MODIFIED SERINE, FORMS A SULFENYL AMIDE BOND WITH CYS 215

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 66.75 %
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 12%PEG, 0.2M MGCL2. PROTEIN WAS OXIDIZED WITH A 1:1.25 MOLAR RATIO OF H2O2 - PROTEIN PRIOR TO CRYSTALLIZATION
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: unknown / Details: Barford, D., (1994) Science, 263, 1397.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES11
20.2 Mmagnesium acetate11
314 %(w/v)PEG800011
410 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 43606 / % possible obs: 99.5 % / Redundancy: 7.07 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 26.26
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 26.26 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 50 Å / Num. measured all: 308523 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.68

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HNP

2hnp


Resolution: 1.8→76.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.093 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: PROTEIN WAS OXIDIZED WITH A 1:1.25 MOLAR RATIO OF H2O2 PROTEIN PRIOR TO CRYSTALLIZATION
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2217 5.1 %RANDOM
Rwork0.203 ---
obs0.204 41389 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 181 2470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212342
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9553158
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.140.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021771
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21062
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 155
Rwork0.254 3020
Refinement
*PLUS
% reflection Rfree: 5.1 % / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.785

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