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- PDB-7l0c: Ligand-free PTP1B T177G -

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Basic information

Entry
Database: PDB / ID: 7l0c
TitleLigand-free PTP1B T177G
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 / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway ...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 / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / cytoplasmic side of endoplasmic reticulum membrane / negative regulation of vascular associated smooth muscle cell migration / positive regulation of IRE1-mediated unfolded protein response / positive regulation of systemic arterial blood pressure / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Regulation of IFNA/IFNB signaling / peptidyl-tyrosine dephosphorylation / regulation of postsynapse assembly / regulation of proteolysis / positive regulation of JUN kinase activity / cellular response to fibroblast growth factor stimulus / growth hormone receptor signaling pathway via JAK-STAT / cellular response to angiotensin / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / negative regulation of MAP kinase activity / cellular response to unfolded protein / regulation of signal transduction / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / positive regulation of cardiac muscle cell apoptotic process / protein dephosphorylation / MECP2 regulates neuronal receptors and channels / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / protein tyrosine phosphatase activity / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / cellular response to nitric oxide / 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 / cellular response to nerve growth factor stimulus / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MET activity / receptor tyrosine kinase binding / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / mitochondrial matrix / cadherin binding / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / 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, 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 / Tyrosine specific protein phosphatases domain profile. / 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: 1.8 Å
AuthorsShen, R.D. / Hengge, A.C. / Johnson, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR01GM112781 United States
CitationJournal: Jacs Au / Year: 2021
Title: Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases.
Authors: Shen, R. / Crean, R.M. / Johnson, S.J. / Kamerlin, S.C.L. / Hengge, A.C.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,2961
Polymers37,2961
Non-polymers00
Water5,008278
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)88.506, 88.506, 104.432
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 37295.551 Da / Num. of mol.: 1 / Mutation: T177G
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M tris hydrochloride pH 7.5-8.5, 0.2 M magnesium acetate tetrahydrate, and 20-25 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 44228 / % possible obs: 99.9 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.03 / Rrim(I) all: 0.132 / Χ2: 1.308 / Net I/σ(I): 5.8 / Num. measured all: 834945
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8614.81.48743250.6990.3971.541.074100
1.86-1.9417.71.15143850.8490.2811.1851.104100
1.94-2.0318.70.83943530.9310.1980.8621.121100
2.03-2.1319.10.58743940.9610.1370.6041.1499.9
2.13-2.2720.40.3844000.9860.0860.391.169100
2.27-2.4419.60.26144070.9920.060.2681.201100
2.44-2.6919.50.17643960.9950.0410.1811.27599.8
2.69-3.0820.20.11844380.9980.0270.1211.368100
3.08-3.8819.70.07244850.9990.0170.0741.656100
3.88-50190.05946450.9990.0140.0611.85599.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XEE

6xee


Resolution: 1.8→44.25 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1748 2003 4.53 %
Rwork0.1631 42190 -
obs0.1636 44193 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.03 Å2 / Biso mean: 29.9711 Å2 / Biso min: 14.13 Å2
Refinement stepCycle: final / Resolution: 1.8→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 0 278 2648
Biso mean---39.82 -
Num. residues----299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.850.29681410.253729583099
1.85-1.90.26261370.207229553092
1.9-1.950.18911400.201929833123
1.95-2.010.20181410.17430003141
2.01-2.090.20191420.178329773119
2.09-2.170.19581440.165429913135
2.17-2.270.21151400.158529993139
2.27-2.390.1851430.161329873130
2.39-2.540.16381420.164930083150
2.54-2.730.17751430.163630083151
2.73-3.010.19721420.180830223164
3.01-3.440.16071460.162530373183
3.45-4.340.15071470.140930773224
4.34-44.250.15081550.151831883343
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3796-0.27880.08670.2136-0.11940.1688-0.0522-0.0088-0.1526-0.05180.0395-0.46520.24840.50480.00040.26480.03060.0660.4556-0.03980.3718-22.677613.79869.311
20.38820.01720.31480.63820.13940.37420.06650.0838-0.1878-0.1831-0.02910.11080.22730.06210.00030.2890.0305-0.01760.1587-0.00250.2395-51.17252.08669.2232
30.84980.14660.2451.28120.45390.56890.02450.0681-0.06830.0590.00480.13840.02170.0580.00010.21170.04130.00120.15720.00840.1714-50.563314.597815.0562
41.53950.040.1821.1560.13830.9563-0.0427-0.02140.00660.00260.0220.099-0.1344-0.0273-0.00040.22350.0510.00290.12420.00790.1685-52.602323.431416.9163
51.22110.10350.07530.9621-0.09771.1246-0.00260.01790.05860.07660.0517-0.1194-0.11360.2183-00.21240.0091-0.0020.1819-0.00210.1804-32.500719.956618.7256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )A1 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 68 )A27 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 119 )A69 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 220 )A120 - 220
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 299 )A221 - 299

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