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- PDB-6cwv: Protein Tyrosine Phosphatase 1B A122S mutant -

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Basic information

Entry
Database: PDB / ID: 6cwv
TitleProtein Tyrosine Phosphatase 1B A122S mutant
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / insulin signaling / diabetes / cancer / signaling
Function / homology
Function and homology information


regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / 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 / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / 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 / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / positive regulation of protein tyrosine kinase activity / 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 / endoplasmic reticulum unfolded protein response / Growth hormone receptor signaling / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / negative regulation of MAP kinase activity / 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 / 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 / Tyrosine specific protein phosphatases active site. ...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
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98002287694 Å
AuthorsHjortness, M. / Zwart, P. / Sankaran, B. / Fox, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1750244 United States
National Science Foundation (NSF, United States)1804897 United States
CitationJournal: Biochemistry / Year: 2018
Title: Evolutionarily Conserved Allosteric Communication in Protein Tyrosine Phosphatases.
Authors: Hjortness, M.K. / Riccardi, L. / Hongdusit, A. / Zwart, P.H. / Sankaran, B. / De Vivo, M. / Fox, J.M.
History
DepositionMar 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 21, 2018Group: Data collection / 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 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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)38,4772
Polymers38,4531
Non-polymers241
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.434, 89.434, 105.554
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

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


Mass: 38452.777 Da / Num. of mol.: 1 / Mutation: A122S
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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.17 Å3/Da / Density % sol: 66.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 200 mM magnesium acetate, and 14% polyethylene glycol 8000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.98→105.55 Å / Num. obs: 34540 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 32.4631722861 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.028 / Net I/σ(I): 16.7
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 2.145 / CC1/2: 0.582 / Rpim(I) all: 0.678

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Processing

Software
NameClassification
DIALSdata collection
xia2data reduction
xia2data scaling
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a5j

3a5j


Resolution: 1.98002287694→44.7169 Å / SU ML: 0.276494433196 / Cross valid method: THROUGHOUT / σ(F): 1.33145488424 / Phase error: 28.5753789808
RfactorNum. reflection% reflectionSelection details
Rfree0.246377958586 1684 4.91463592587 %RANDOM
Rwork0.204635027207 ---
obs0.206665454083 34265 99.2958154631 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.2253048481 Å2
Refinement stepCycle: LAST / Resolution: 1.98002287694→44.7169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 1 220 2519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007547781806832419
X-RAY DIFFRACTIONf_angle_d0.8184595269543277
X-RAY DIFFRACTIONf_chiral_restr0.0517058092853349
X-RAY DIFFRACTIONf_plane_restr0.00496483961505427
X-RAY DIFFRACTIONf_dihedral_angle_d2.981472528182068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.03830.3971789976481640.3725527367762612X-RAY DIFFRACTION97.7809087707
2.0383-2.10410.3587043683161340.332791390932678X-RAY DIFFRACTION99.3990809473
2.1041-2.17930.3718682004361440.3210654876352673X-RAY DIFFRACTION99.0854730918
2.1793-2.26650.3553034682811330.2701793265022670X-RAY DIFFRACTION99.467707594
2.2665-2.36970.3505008355431480.2700851771752692X-RAY DIFFRACTION99.1620111732
2.3697-2.49460.2906222219921480.2472890215772692X-RAY DIFFRACTION99.4397759104
2.4946-2.65090.2584554082381180.2318656088472703X-RAY DIFFRACTION99.2960225273
2.6509-2.85550.2635109592251490.2233784445522698X-RAY DIFFRACTION99.5106606082
2.8555-3.14280.2831471457091170.2213260809682756X-RAY DIFFRACTION99.2400690846
3.1428-3.59740.212959130661410.1862433517962749X-RAY DIFFRACTION99.8963014172
3.5974-4.53170.2042527982061260.1450413020262784X-RAY DIFFRACTION99.7942386831
4.5317-44.72830.1803670377161620.160876864842874X-RAY DIFFRACTION99.4757536042

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