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- PDB-6xea: Crystal Structure of the PTP1B YopH WPD loop Chimera 3 bound to v... -

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Basic information

Entry
Database: PDB / ID: 6xea
TitleCrystal Structure of the PTP1B YopH WPD loop Chimera 3 bound to vanadate
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PTP1B / tyrosine phosphatase / WPD loop
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 / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of systemic arterial blood pressure / 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 / MECP2 regulates neuronal receptors and channels / protein dephosphorylation / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / Integrin signaling / protein tyrosine phosphatase activity / 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
BENZAMIDINE / VANADATE ION / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.549 Å
AuthorsOlsen, K.J. / Shen, R. / Johnson, S.J. / Hengge, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112781 United States
CitationJournal: Chem Sci / Year: 2022
Title: Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases.
Authors: Shen, R. / Crean, R.M. / Olsen, K.J. / Corbella, M. / Calixto, A.R. / Richan, T. / Brandao, T.A.S. / Berry, R.D. / Tolman, A. / Loria, J.P. / Johnson, S.J. / Kamerlin, S.C.L. / Hengge, A.C.
History
DepositionJun 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: 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 25, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7135
Polymers37,3321
Non-polymers3824
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.586, 88.586, 104.658
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37331.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18031, protein-tyrosine-phosphatase

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Non-polymers , 5 types, 217 molecules

#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.28 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: tris hydrochloride pH 8.2, magnesium acetate tetrahydrate, PEG 8000 and benzamidine
PH range: 7.8-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.549→50 Å / Num. obs: 67840 / % possible obs: 97.6 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.017 / Rrim(I) all: 0.073 / Χ2: 1.027 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.6111.61.07364930.7260.3161.1211.10394.4
1.61-1.6717.60.8666710.8940.2070.8851.09597.3
1.67-1.7518.90.62967100.9510.1460.6461.08497.5
1.75-1.8418.50.39667380.9780.0930.4071.03697.8
1.84-1.9518.40.24466430.9890.0570.2511.01396.5
1.95-2.119.60.16368240.9950.0370.1671.00498.3
2.1-2.3219.20.11668350.9970.0270.1190.98298.7
2.32-2.6519.10.08868100.9980.020.090.94597.7
2.65-3.3419.40.06769730.9990.0150.0691.0999.3
3.34-5018.80.04871430.9990.0110.0490.96398.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.11 Å44.29 Å
Translation6.11 Å44.29 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.1phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QKP

3qkp


Resolution: 1.549→44.293 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 3428 5.05 %
Rwork0.1868 64395 -
obs0.1874 67823 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.34 Å2 / Biso mean: 32.4575 Å2 / Biso min: 15.36 Å2
Refinement stepCycle: final / Resolution: 1.549→44.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 23 213 2661
Biso mean--33.3 39.35 -
Num. residues----299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.549-1.57070.32231380.2951260696
1.5707-1.59420.29731290.2864250791
1.5942-1.61910.2711500.2603259597
1.6191-1.64570.26771440.2561266997
1.6457-1.6740.30561410.2637265897
1.674-1.70450.32121430.2642264898
1.7045-1.73730.23641410.2468265897
1.7373-1.77270.23691360.2393265098
1.7727-1.81130.23831360.2242265198
1.8113-1.85340.23551400.2208267898
1.8534-1.89970.2351460.2113255494
1.8997-1.95110.23021450.2073268798
1.9511-2.00850.20611470.2071268998
2.0085-2.07340.22671460.2078270799
2.0734-2.14750.23511630.2014266098
2.1475-2.23340.18951380.1848271599
2.2334-2.33510.18821450.1956271199
2.3351-2.45820.20651480.1906263896
2.4582-2.61220.19871290.196274499
2.6122-2.81380.2051460.188274399
2.8138-3.09690.1911470.1931276399
3.0969-3.54490.1941490.1823274398
3.5449-4.46550.18741440.14592813100
4.4655-44.2930.14311370.1597290898

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