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- PDB-8u1e: Apo protein tyrosine phosphatase 1B (PTP1B) at high resolution (1... -

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Basic information

Entry
Database: PDB / ID: 8u1e
TitleApo protein tyrosine phosphatase 1B (PTP1B) at high resolution (1.43 A) in space group P43212 with two distinctly ordered chains
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / Highest resolution apo-PTP1B structure
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 insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / 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, 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: 1.43 Å
AuthorsSharma, S. / Mehlman, S.T. / Keedy, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)NIH R35GM133769 United States
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2024
Title: High-resolution double vision of the allosteric phosphatase PTP1B.
Authors: Sharma, S. / Skaist Mehlman, T. / Sagabala, R.S. / Boivin, B. / Keedy, D.A.
#1: Journal: Biorxiv / Year: 2023
Title: High-resolution double vision of the archetypal protein tyrosine phosphatase
Authors: Sharma, S. / Mehlman, S.T. / Keedy, D.A.
History
DepositionAug 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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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
B: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1854
Polymers77,1362
Non-polymers492
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.412, 88.412, 163.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 1


Mass: 38567.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P18031
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.21 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MgCl2, 0.1 M Hepes pH 7.0, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.43→30.59 Å / Num. obs: 119377 / % possible obs: 97.94 % / Redundancy: 25.6 % / Biso Wilson estimate: 24.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.029 / Rrim(I) all: 0.15 / Net I/σ(I): 10.82
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 25.7 % / Rmerge(I) obs: 9.777 / Mean I/σ(I) obs: 0.31 / Num. unique obs: 11763 / CC1/2: 0.404 / Rpim(I) all: 1.955 / Rrim(I) all: 9.974 / % possible all: 85.28

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS3.71data reduction
DIALS3.7.1data scaling
Coot0.9.8.2model building
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→30.59 Å / SU ML: 0.2311 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5865
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2025 5855 5 %
Rwork0.1497 111181 -
obs0.1523 117036 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.72 Å2
Refinement stepCycle: LAST / Resolution: 1.43→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 2 389 5005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00985214
X-RAY DIFFRACTIONf_angle_d1.0417093
X-RAY DIFFRACTIONf_chiral_restr0.0794743
X-RAY DIFFRACTIONf_plane_restr0.0108936
X-RAY DIFFRACTIONf_dihedral_angle_d5.5737726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.41671340.36063011X-RAY DIFFRACTION80.46
1.45-1.460.39521570.36223148X-RAY DIFFRACTION84.29
1.46-1.480.3731890.33543393X-RAY DIFFRACTION91.1
1.48-1.50.36281890.31593538X-RAY DIFFRACTION94.43
1.5-1.520.31682100.30333580X-RAY DIFFRACTION96.27
1.52-1.540.34571840.2873603X-RAY DIFFRACTION97.23
1.54-1.560.32482080.25913672X-RAY DIFFRACTION97.73
1.56-1.590.33772130.24813631X-RAY DIFFRACTION98.44
1.59-1.610.28271990.21433750X-RAY DIFFRACTION99.97
1.61-1.640.28211970.2043741X-RAY DIFFRACTION99.97
1.64-1.670.23991970.20173771X-RAY DIFFRACTION100
1.67-1.70.25771920.20033751X-RAY DIFFRACTION100
1.7-1.730.26121850.19683741X-RAY DIFFRACTION100
1.73-1.760.28992080.20343739X-RAY DIFFRACTION99.97
1.76-1.80.29631640.19643790X-RAY DIFFRACTION100
1.8-1.840.21722120.16193756X-RAY DIFFRACTION99.82
1.84-1.890.18871840.14313729X-RAY DIFFRACTION99.54
1.89-1.940.20522290.13353749X-RAY DIFFRACTION100
1.94-20.21131830.13013789X-RAY DIFFRACTION100
2-2.060.20252010.13543771X-RAY DIFFRACTION99.97
2.06-2.140.19971840.13693779X-RAY DIFFRACTION100
2.14-2.220.17742090.12633775X-RAY DIFFRACTION100
2.22-2.320.16832150.11913796X-RAY DIFFRACTION100
2.32-2.440.20141940.123782X-RAY DIFFRACTION99.57
2.44-2.60.17721970.12333823X-RAY DIFFRACTION100
2.6-2.80.21022070.14123813X-RAY DIFFRACTION100
2.8-3.080.22191900.14623857X-RAY DIFFRACTION99.98
3.08-3.520.19132100.1463860X-RAY DIFFRACTION99.73
3.53-4.440.15011940.12683940X-RAY DIFFRACTION100
4.44-30.590.18962200.14944103X-RAY DIFFRACTION99.49

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