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- PDB-1oeo: PTP1B with the catalytic cysteine oxidized to sulfonic acid -

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Basic information

Entry
Database: PDB / ID: 1oeo
TitlePTP1B with the catalytic cysteine oxidized to sulfonic acid
ComponentsPROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1
KeywordsHYDROLASE / PHOSPHORYLATION / CYSTEINE SULFONIC ACID
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
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, 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 / Tyrosine specific protein phosphatases domain profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,4141
Polymers37,4141
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.365, 88.365, 104.764
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: 37413.637 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-321
Source method: isolated from a genetically manipulated source
Details: CATALYTIC CYSTEINE X215 IS OXIDIZED TO A SULFONIC ACID
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES HYDROLYSIS OF PROTEIN TYROSINE PHOSPHATE TO PROTEIN TYROSINE ANDPHOSPHATE.

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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: 3.27 Å3/Da / Density % sol: 62.09 %
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 12%PEG, 0.2M MGCL2,CRYSTALS WERE SOAKED OVERNIGHT IN 100 MICROMOLAR PERVANADATE PRIOR TO DATA COLLECTION
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: ROTATING ANODE / Wavelength: 1.541
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2002 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. obs: 26299 / % possible obs: 98.1 % / Redundancy: 6.98 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.68
Reflection shellResolution: 2.15→2.2 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.97 / % possible all: 96.7
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 25 Å / Num. measured all: 183671 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.97

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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: 2.15→76.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.676 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1305 5.1 %RANDOM
Rwork0.182 ---
obs0.184 24459 98.1 %-
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: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.21 Å20 Å2
2--0.43 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.15→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 0 153 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212342
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.9513155
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415277
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_restr0.1540.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021761
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21036
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3131.51397
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45822260
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8833945
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3114.5895
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: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 107
Rwork0.202 1757
Refinement
*PLUS
% reflection Rfree: 5.1 % / Rfactor Rfree: 0.215 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.026
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.894

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