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- PDB-1ptv: CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 1ptv
TitleCRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH PHOSPHOTYROSINE
ComponentsPROTEIN TYROSINE PHOSPHATASE 1B
KeywordsCOMPLEX (HYDROLASE/PEPTIDE) / HYDROLASE / ACETYLATION / PHOSPHORYLATION / COMPLEX (HYDROLASE-PEPTIDE) COMPLEX
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 / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / 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 / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / cytoplasmic side of endoplasmic reticulum membrane / 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 / positive regulation of JUN kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / negative regulation of MAP kinase activity / regulation of endocytosis / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / cellular response to angiotensin / regulation of proteolysis / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / growth hormone receptor signaling pathway via JAK-STAT / cellular response to unfolded protein / regulation of signal transduction / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNG signaling / negative regulation of signal transduction / Growth hormone receptor signaling / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cardiac muscle cell apoptotic process / endoplasmic reticulum unfolded protein response / protein dephosphorylation / MECP2 regulates neuronal receptors and channels / Insulin receptor recycling / cellular response to fibroblast growth factor stimulus / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / Integrin signaling / protein-tyrosine-phosphatase / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / response to nutrient levels / insulin receptor binding / cellular response to nerve growth factor stimulus / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / cadherin binding / mitochondrial matrix / 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 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
O-PHOSPHOTYROSINE / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBarford, D. / Jia, Z.
Citation
Journal: Science / Year: 1995
Title: Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B.
Authors: Jia, Z. / Barford, D. / Flint, A.J. / Tonks, N.K.
#1: Journal: Science / Year: 1994
Title: Crystal Structure of Human Protein Tyrosine Phosphatase 1B
Authors: Barford, D. / Flint, A.J. / Tonks, N.K.
History
DepositionApr 21, 1995Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN TYROSINE PHOSPHATASE 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6112
Polymers37,3501
Non-polymers2611
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.200, 88.200, 103.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN TYROSINE PHOSPHATASE 1B


Mass: 37349.570 Da / Num. of mol.: 1 / Mutation: C215S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PTR / O-PHOSPHOTYROSINE / PHOSPHONOTYROSINE


Type: L-peptide linking / Mass: 261.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CATALYTIC RESIDUE IS CYS 215. IN THIS ENTRY RESIDUE 215 IS SER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / Details: Barford, D., (1994) J. Mol. Biol., 239, 726.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlPTP1B1drop
20.1 MHEPES1reservoir
30.2 Mmagnesium acetate1reservoir
412-16 %(w/v)PEG80001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Feb 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21436 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.035
Reflection
*PLUS
Num. measured all: 146758

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.172 --
obs0.172 19460 97.8 %
Displacement parametersBiso mean: 25.9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 17 259 2702
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.92
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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