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- PDB-7mou: PTP1B F225Y-R199N-L195R -

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Basic information

Entry
Database: PDB / ID: 7mou
TitlePTP1B F225Y-R199N-L195R
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PROTEIN TYROSINE 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 / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome ...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 / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / mitochondrial crista / cytoplasmic side of endoplasmic reticulum membrane / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of JUN kinase activity / positive regulation of systemic arterial blood pressure / negative regulation of MAP kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNA/IFNB signaling / regulation of proteolysis / cellular response to angiotensin / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of cell-substrate adhesion / cellular response to unfolded protein / regulation of signal transduction / Regulation of IFNG signaling / negative regulation of signal transduction / Growth hormone receptor signaling / positive regulation of heart rate / positive regulation of cardiac muscle cell apoptotic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein dephosphorylation / endoplasmic reticulum unfolded protein response / MECP2 regulates neuronal receptors and channels / ephrin receptor binding / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / cellular response to fibroblast growth factor stimulus / Integrin signaling / protein-tyrosine-phosphatase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to nitric oxide / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / 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 / Negative regulation of MET activity / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 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, 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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
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: 1.48 Å
AuthorsTorgeson, K.R. / Page, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
American Diabetes Association1-14-ACN-31 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM09482 United States
CitationJournal: Sci Adv / Year: 2022
Title: Conserved conformational dynamics determine enzyme activity.
Authors: Torgeson, K.R. / Clarkson, M.W. / Granata, D. / Lindorff-Larsen, K. / Page, R. / Peti, W.
History
DepositionMay 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9637
Polymers33,5501
Non-polymers4136
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.427, 88.427, 72.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 33550.340 Da / Num. of mol.: 1 / Mutation: F225Y, R199N, L195R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, .1 M Tris pH 7.8, 16.5% PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.48→38.29 Å / Num. obs: 54819 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 15.62 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.2
Reflection shellResolution: 1.48→1.5 Å / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2649 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k9v

5k9v


Resolution: 1.48→38.29 Å / SU ML: 0.1431 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.4379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1801 2735 4.99 %
Rwork0.1715 52053 -
obs0.1719 54788 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.37 Å2
Refinement stepCycle: LAST / Resolution: 1.48→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 23 229 2524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01362449
X-RAY DIFFRACTIONf_angle_d1.31823323
X-RAY DIFFRACTIONf_chiral_restr0.1102354
X-RAY DIFFRACTIONf_plane_restr0.0109432
X-RAY DIFFRACTIONf_dihedral_angle_d13.8972940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.25291410.22952538X-RAY DIFFRACTION98.53
1.5-1.530.20061490.20912526X-RAY DIFFRACTION99.48
1.53-1.560.22071280.19792594X-RAY DIFFRACTION99.67
1.56-1.590.21871410.18862547X-RAY DIFFRACTION99.7
1.59-1.630.22591420.18772598X-RAY DIFFRACTION99.78
1.63-1.670.21221350.17962566X-RAY DIFFRACTION99.82
1.67-1.710.22721280.17992606X-RAY DIFFRACTION99.89
1.71-1.750.18181500.17182546X-RAY DIFFRACTION99.81
1.75-1.810.17061580.16822588X-RAY DIFFRACTION99.89
1.81-1.860.18521400.15592563X-RAY DIFFRACTION99.96
1.86-1.930.17751240.16112623X-RAY DIFFRACTION100
1.93-2.010.20411200.1682614X-RAY DIFFRACTION99.96
2.01-2.10.18411310.15052606X-RAY DIFFRACTION100
2.1-2.210.16261050.15162623X-RAY DIFFRACTION100
2.21-2.350.17951300.15552621X-RAY DIFFRACTION100
2.35-2.530.19441340.16992625X-RAY DIFFRACTION100
2.53-2.780.18961540.18562626X-RAY DIFFRACTION100
2.79-3.190.2231350.18672629X-RAY DIFFRACTION100
3.19-4.010.14631230.16292670X-RAY DIFFRACTION100
4.01-38.290.14561670.17312744X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: -28.8194452984 Å / Origin y: -14.2784913013 Å / Origin z: -7.92367376281 Å
111213212223313233
T0.127054871933 Å20.0224603613343 Å2-0.0243889820244 Å2-0.113642136242 Å20.00504111919745 Å2--0.103654862173 Å2
L1.13159520366 °2-0.358019416399 °20.0732258780794 °2-1.50720326748 °20.111817964012 °2--0.844426588456 °2
S-0.0537423801498 Å °-0.0309754375784 Å °0.0946185655884 Å °0.150858628204 Å °0.0492400101672 Å °-0.167102577606 Å °-0.022535599449 Å °0.114150286555 Å °0.00038702047807 Å °
Refinement TLS groupSelection details: all

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