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- PDB-7mne: PTP1B P206G mutation, open state -

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Basic information

Entry
Database: PDB / ID: 7mne
TitlePTP1B P206G mutation, open 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 / 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: 1.6 Å
AuthorsTorgeson, K.R. / Page, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
American Diabetes Association1-14-ACN-31 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098482 United States
CitationJournal: Sci Adv / Year: 2022
Title: Conserved conformational dynamics determine enzyme activity.
Authors: Torgeson, K.R. / Clarkson, M.W. / Granata, D. / Lindorff-Larsen, K. / Page, R. / Peti, W.
History
DepositionApr 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2979
Polymers35,7571
Non-polymers5408
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.123, 88.123, 72.377
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#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: 35756.684 Da / Num. of mol.: 1 / Mutation: P206G
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 0.1 M Tris pH 7.8, 17% PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→38.16 Å / Num. obs: 41756 / % possible obs: 96.4 % / Redundancy: 8.1 % / Biso Wilson estimate: 17.57 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.5
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1483 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k9v

5k9v


Resolution: 1.6→38.16 Å / SU ML: 0.1787 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.5369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1761 1967 4.72 %
Rwork0.1632 39686 -
obs0.1639 41653 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.86 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 30 179 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01472399
X-RAY DIFFRACTIONf_angle_d1.49443250
X-RAY DIFFRACTIONf_chiral_restr0.089347
X-RAY DIFFRACTIONf_plane_restr0.0082421
X-RAY DIFFRACTIONf_dihedral_angle_d16.3989917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.2533930.23492104X-RAY DIFFRACTION71.49
1.64-1.680.2341280.20662527X-RAY DIFFRACTION86.68
1.68-1.730.19631240.18492704X-RAY DIFFRACTION92
1.73-1.790.20291430.1652750X-RAY DIFFRACTION95.57
1.79-1.850.19781480.1562894X-RAY DIFFRACTION98.77
1.85-1.930.2121340.15772946X-RAY DIFFRACTION99.61
1.93-2.010.1981380.15432938X-RAY DIFFRACTION100
2.01-2.120.19191390.15022935X-RAY DIFFRACTION99.93
2.12-2.250.17761260.14692945X-RAY DIFFRACTION99.84
2.25-2.430.16871550.16482953X-RAY DIFFRACTION100
2.43-2.670.20391700.17022922X-RAY DIFFRACTION99.97
2.67-3.060.18931340.17712988X-RAY DIFFRACTION100
3.06-3.850.16611500.15622998X-RAY DIFFRACTION99.94
3.85-38.160.1421850.15943082X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -26.9463848598 Å / Origin y: 18.0032837595 Å / Origin z: 4.19167078407 Å
111213212223313233
T0.151009177744 Å2-0.0208371216044 Å2-0.0143425586603 Å2-0.113778825656 Å20.0240394905716 Å2--0.122606735884 Å2
L1.39134877536 °20.245495346184 °20.157192932321 °2-1.51890736304 °2-0.0205066849947 °2--0.776393825222 °2
S0.0671474496127 Å °-0.0598281319651 Å °-0.151850616549 Å °0.118654925689 Å °-0.0617902085209 Å °-0.204340383877 Å °0.0424909179607 Å °0.0573925280539 Å °-0.00376984079653 Å °
Refinement TLS groupSelection details: all

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