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- PDB-7mov: PTP1B 1-301 F225Y-R199N mutations -

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Basic information

Entry
Database: PDB / ID: 7mov
TitlePTP1B 1-301 F225Y-R199N mutations
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: 1.65 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
DepositionMay 3, 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
B: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,68916
Polymers71,5392
Non-polymers1,14914
Water8,845491
1
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1527
Polymers35,7701
Non-polymers3836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5369
Polymers35,7701
Non-polymers7678
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.359, 90.102, 74.490
Angle α, β, γ (deg.)90.000, 110.933, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 35769.656 Da / Num. of mol.: 2 / Mutation: F225Y, R199N
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 7.4, 0.2 M Magnesium Chloride, 21.5% PEG 8000

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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: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.65→37.82 Å / Num. obs: 80907 / % possible obs: 95.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.8
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 1.004 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3446 / CC1/2: 0.732

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k9v

5k9v


Resolution: 1.65→37.82 Å / SU ML: 0.1676 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1933 4057 5.02 %
Rwork0.1653 76826 -
obs0.1667 80883 95.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.89 Å2
Refinement stepCycle: LAST / Resolution: 1.65→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4465 0 71 491 5027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01854799
X-RAY DIFFRACTIONf_angle_d1.46446507
X-RAY DIFFRACTIONf_chiral_restr0.1026696
X-RAY DIFFRACTIONf_plane_restr0.0134840
X-RAY DIFFRACTIONf_dihedral_angle_d14.48861806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.31181260.27522296X-RAY DIFFRACTION82.61
1.67-1.690.27681150.25322522X-RAY DIFFRACTION90.34
1.69-1.710.28121390.23722652X-RAY DIFFRACTION96.34
1.71-1.730.26511630.22552688X-RAY DIFFRACTION96.09
1.73-1.760.24321260.19712597X-RAY DIFFRACTION95.78
1.76-1.780.2441460.19542677X-RAY DIFFRACTION96.48
1.78-1.810.22241630.19972655X-RAY DIFFRACTION95.92
1.81-1.840.24941620.19472618X-RAY DIFFRACTION96.23
1.84-1.870.2471400.19762712X-RAY DIFFRACTION96.25
1.87-1.90.21121250.19362632X-RAY DIFFRACTION95.96
1.9-1.930.2211410.18252677X-RAY DIFFRACTION95.98
1.93-1.970.21921470.18292651X-RAY DIFFRACTION94.72
1.97-2.010.19881290.16552388X-RAY DIFFRACTION86.7
2.01-2.050.18491420.15842664X-RAY DIFFRACTION96.86
2.05-2.10.18531630.15712680X-RAY DIFFRACTION97.06
2.1-2.150.18011170.1552754X-RAY DIFFRACTION97.26
2.15-2.210.17931460.15252710X-RAY DIFFRACTION97.41
2.21-2.280.20211560.15712669X-RAY DIFFRACTION97.45
2.28-2.350.19431460.16282716X-RAY DIFFRACTION97.18
2.35-2.430.20911390.15292677X-RAY DIFFRACTION96.64
2.43-2.530.17251310.15952608X-RAY DIFFRACTION94.09
2.53-2.650.20121300.16592550X-RAY DIFFRACTION91.5
2.65-2.790.21661320.16242750X-RAY DIFFRACTION98.13
2.79-2.960.19411610.1642712X-RAY DIFFRACTION98.46
2.96-3.190.18631240.16182777X-RAY DIFFRACTION97.91
3.19-3.510.16591200.1522723X-RAY DIFFRACTION96.87
3.51-4.020.17151530.14662569X-RAY DIFFRACTION92.21
4.02-5.060.1651410.14262777X-RAY DIFFRACTION98.68
5.06-37.820.19151340.18452725X-RAY DIFFRACTION94.64
Refinement TLS params.Method: refined / Origin x: 4.92223210396 Å / Origin y: 22.4793106674 Å / Origin z: 21.8370154326 Å
111213212223313233
T0.187262735533 Å20.0111048100744 Å20.0163290953833 Å2-0.15267625965 Å20.00426649829436 Å2--0.136058429878 Å2
L0.959389865255 °20.650491582124 °20.281372656335 °2-0.624307067158 °20.144940500234 °2--0.233101017869 °2
S0.0613160872764 Å °-0.0704741484814 Å °-0.00953491690872 Å °0.0737793937065 Å °-0.0172690669499 Å °-0.0149630268106 Å °0.00983499147976 Å °-0.0533835499935 Å °-0.0475008892627 Å °
Refinement TLS groupSelection details: all

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