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- PDB-5ka7: Protein Tyrosine Phosphatase 1B T178A mutant in complex with TCS4... -

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Basic information

Entry
Database: PDB / ID: 5ka7
TitleProtein Tyrosine Phosphatase 1B T178A mutant in complex with TCS401, closed state
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 / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / positive regulation of protein tyrosine kinase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / cellular response to unfolded protein / regulation of signal transduction / 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 / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / negative regulation of MAP kinase activity / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / protein dephosphorylation / ephrin receptor binding / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein phosphatase 2A binding / endosome lumen / insulin receptor binding / Negative regulation of MET activity / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / 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 superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-OTA / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.061 Å
AuthorsChoy, M.S. / Peti, W. / Page, R.
CitationJournal: Mol. Cell / Year: 2017
Title: Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.
Authors: Choy, M.S. / Li, Y. / Machado, L.E. / Kunze, M.B. / Connors, C.R. / Wei, X. / Lindorff-Larsen, K. / Page, R. / Peti, W.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,1769
Polymers35,5141
Non-polymers6628
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.564, 88.564, 104.110
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: 35514.477 Da / Num. of mol.: 1 / Mutation: T78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase

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Non-polymers , 5 types, 173 molecules

#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-OTA / 2-(OXALYL-AMINO)-4,5,6,7-TETRAHYDRO-THIENO[2,3-C]PYRIDINE-3-CARBOXYLIC ACID


Mass: 270.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O5S
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.1 M Tris, pH 7.6, 0.2 M MgCl2, 24% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 29148 / % possible obs: 98.2 % / Redundancy: 10.8 % / Biso Wilson estimate: 26.12 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.012 / Net I/av σ(I): 35.728 / Net I/σ(I): 9.6 / Num. measured all: 315712
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.06-2.18.90.3913920.88794.6
2.1-2.1310.30.35414210.89496.9
2.13-2.1711.10.30914020.88396.9
2.17-2.22110.27114150.90497.3
2.22-2.27110.26614520.9197.5
2.27-2.32110.24914180.94197.6
2.32-2.38110.2314220.92497.7
2.38-2.44110.1914450.94698.1
2.44-2.5111.10.1814270.9597.9
2.51-2.6110.15814480.95798.1
2.6-2.69110.14214560.96998.4
2.69-2.8110.12814481.00698.8
2.8-2.92110.1114491.02998.5
2.92-3.08110.08714731.09298.9
3.08-3.2711.10.0714721.0799.1
3.27-3.52110.05314821.17199.4
3.52-3.88110.04514941.31699.5
3.88-4.4410.90.03815061.12199.7
4.44-5.5910.80.03415191.09699.7
5.59-5010.20.03216071.10799.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.06 Å44.28 Å
Translation2.06 Å44.28 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C88

1c88


Resolution: 2.061→44.282 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1434 4.95 %
Rwork0.1834 27518 -
obs0.1849 28952 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.34 Å2 / Biso mean: 29.1872 Å2 / Biso min: 11.82 Å2
Refinement stepCycle: final / Resolution: 2.061→44.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 37 165 2601
Biso mean--30.49 31.74 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012489
X-RAY DIFFRACTIONf_angle_d1.0833360
X-RAY DIFFRACTIONf_chiral_restr0.059356
X-RAY DIFFRACTIONf_plane_restr0.007432
X-RAY DIFFRACTIONf_dihedral_angle_d12.9161512
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0613-2.1350.23621380.19942665280396
2.135-2.22040.2351640.18892655281997
2.2204-2.32150.25541660.19642704287098
2.3215-2.44390.24371340.20252733286798
2.4439-2.5970.26091470.20472721286898
2.597-2.79740.3211360.2182720285697
2.7974-3.07890.26881420.22332707284996
3.0789-3.52430.19521270.1872821294899
3.5243-4.43960.18211550.15012821297699
4.4396-44.29220.14611250.16342971309699

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