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- PDB-9cyr: Crystal structure of D245G mutant human PTP1B (PTPN1) at room tem... -

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Basic information

Entry
Database: PDB / ID: 9cyr
TitleCrystal structure of D245G mutant human PTP1B (PTPN1) at room temperature (298 K)
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PTP1B / Phosphatase / Allostery / PTP
Function / homology
Function and homology information


regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / 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 / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / 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 / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / 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 / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of MAP kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / 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 / 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEbrahim, A. / Perdikari, A. / Woods, V.A. / Lawler, K. / Bounds, R. / Singh, N.I. / Mehlman, T. / Riley, B.T. / Sharma, S. / Morris, J.W. ...Ebrahim, A. / Perdikari, A. / Woods, V.A. / Lawler, K. / Bounds, R. / Singh, N.I. / Mehlman, T. / Riley, B.T. / Sharma, S. / Morris, J.W. / Keogh, J.M. / Henning, E. / Smith, M. / Farooqi, I.S. / Keedy, D.A.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133769 United States
Wellcome Trust207462/Z/17/Z United Kingdom
CitationJournal: Biorxiv / Year: 2024
Title: Structures of human PTP1B variants reveal allosteric sites to target for weight loss therapy
Authors: Perdikari, A. / Woods, V. / Ebrahim, A. / Lawler, K. / Bounds, R. / Singh, N. / Mehlman, T. / Riley, B. / Sharma, S. / Morris, J. / Keogh, J. / Henning, E. / Smith, M. / Farooqi, I. / Keedy, D.
History
DepositionAug 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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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)37,4103
Polymers37,3081
Non-polymers1022
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.579, 89.579, 106.234
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#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: 37307.602 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 (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.3 Å3/Da / Density % sol: 67.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13.5% PEG 8000, 2% ethanol

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.65→38.79 Å / Num. obs: 59663 / % possible obs: 99.88 % / Redundancy: 9.7 % / Biso Wilson estimate: 30.81 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0526 / Rpim(I) all: 0.01753 / Rrim(I) all: 0.05551 / Net I/σ(I): 16.67
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.719 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 5868 / CC1/2: 0.417 / CC star: 0.768 / Rpim(I) all: 0.6797 / Rrim(I) all: 1.853 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS3.7.1data reduction
Aimless0.8.2data scaling
MOLREP11phasing
REFMAC5.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→38.79 Å / SU ML: 0.2697 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.6363
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 2943 4.93 %
Rwork0.1665 56717 -
obs0.1674 59660 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.24 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 5 140 2455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152478
X-RAY DIFFRACTIONf_angle_d1.12423353
X-RAY DIFFRACTIONf_chiral_restr0.0638352
X-RAY DIFFRACTIONf_plane_restr0.0093439
X-RAY DIFFRACTIONf_dihedral_angle_d5.9061336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.3721530.32972623X-RAY DIFFRACTION98.97
1.68-1.710.3321350.31522647X-RAY DIFFRACTION99.25
1.71-1.740.36241430.31072668X-RAY DIFFRACTION99.82
1.74-1.770.34281410.3192645X-RAY DIFFRACTION100
1.77-1.810.30541390.30342719X-RAY DIFFRACTION99.97
1.81-1.850.31021180.26412669X-RAY DIFFRACTION100
1.85-1.890.23981430.23672679X-RAY DIFFRACTION99.96
1.89-1.940.23031460.20752679X-RAY DIFFRACTION100
1.94-1.990.22011340.19522686X-RAY DIFFRACTION99.96
1.99-2.050.21981760.19052653X-RAY DIFFRACTION100
2.05-2.110.2131190.19642711X-RAY DIFFRACTION100
2.11-2.190.24531490.20982673X-RAY DIFFRACTION100
2.19-2.280.24021260.17212691X-RAY DIFFRACTION100
2.28-2.380.21021530.17882691X-RAY DIFFRACTION100
2.38-2.510.21641190.1662735X-RAY DIFFRACTION100
2.51-2.660.18111470.16972683X-RAY DIFFRACTION100
2.66-2.870.20571430.17242718X-RAY DIFFRACTION99.97
2.87-3.160.19621380.17082743X-RAY DIFFRACTION100
3.16-3.610.15451380.15782743X-RAY DIFFRACTION100
3.61-4.550.12951320.11662778X-RAY DIFFRACTION100
4.55-38.790.14621510.1392883X-RAY DIFFRACTION99.87

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