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- PDB-3qkq: Protein Tyrosine Phosphatase 1B - W179F mutant bound with vanadate -

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Basic information

Entry
Database: PDB / ID: 3qkq
TitleProtein Tyrosine Phosphatase 1B - W179F mutant bound with vanadate
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / P-loop / WPD-loop / Vanadate / Protein Phosphatase / EGFR receptor / Phosphoprotein
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 / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane ...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 / 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 / positive regulation of IRE1-mediated unfolded protein response / 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 / regulation of signal transduction / cellular response to unfolded protein / 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 / ephrin receptor binding / protein dephosphorylation / 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
VANADATE ION / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsBrandao, T.A.S. / Johnson, S.J. / Hengge, A.C.
CitationJournal: Arch.Biochem.Biophys. / Year: 2012
Title: The molecular details of WPD-loop movement differ in the protein-tyrosine phosphatases YopH and PTP1B.
Authors: Brandao, T.A. / Johnson, S.J. / Hengge, A.C.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)37,8406
Polymers37,3271
Non-polymers5135
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.620, 88.620, 104.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 37326.605 Da / Num. of mol.: 1 / Fragment: Catalytic domain, residues 1-321 / Mutation: W179F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ptp1b, ptpn1 / Plasmid: pEt-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#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.: 276 / 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: 61.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2uL of protein solution, 0.5 uL sucrose 30 % (w/v) and 3 uL of precipitant solution (0.1 M Hepes pH 7.5, 0.2 M magnesium acetate and 15-20 % polyethylene glycol 8000). The protein solution ...Details: 2uL of protein solution, 0.5 uL sucrose 30 % (w/v) and 3 uL of precipitant solution (0.1 M Hepes pH 7.5, 0.2 M magnesium acetate and 15-20 % polyethylene glycol 8000). The protein solution was prepared with 15 uL of 12 mg/mL PTP1B W179F in 10 mM Tris pH 7.5, 25 mM NaCl, 0.2 mM EDTA and 3 mM DTT, and 0.5 uL of 60 mM of sodium vanadate. The well solution was 500 uL of precipitant solution., vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 8, 2009 / Details: mirrors
RadiationMonochromator: Osmic Blue Optics / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→38.37 Å / Num. all: 24220 / Num. obs: 24220 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.51 % / Biso Wilson estimate: 36.11 Å2 / Rmerge(I) obs: 0.108 / Χ2: 0.97 / Net I/σ(I): 7.9 / Scaling rejects: 1009
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.285.610.4942.71321023511.1597.3
2.28-2.375.60.4572.91323323601.1297.6
2.37-2.485.60.4143.31332223761.1298.3
2.48-2.615.60.3683.61337423841.0898.1
2.61-2.775.570.3174.11339724021.0698.8
2.77-2.995.530.2415.11341324191.0198.8
2.99-3.295.520.1537.31345224280.9399.3
3.29-3.765.480.086121346224330.8199.4
3.76-4.745.420.05218.61380924900.799.7
4.74-38.375.220.04919.41385225770.799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.2 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.37 Å
Translation2.5 Å38.37 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CM2 with the active site water molecules removed

2cm2


Resolution: 2.2→38.37 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8381 / SU ML: 0.33 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1237 5.11 %Random
Rwork0.1959 ---
all0.1987 24208 --
obs0.1987 24208 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.402 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 150.9 Å2 / Biso mean: 43.009 Å2 / Biso min: 18.23 Å2
Baniso -1Baniso -2Baniso -3
1--2.4423 Å2-0 Å20 Å2
2---2.4423 Å20 Å2
3---4.8847 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 31 276 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092571
X-RAY DIFFRACTIONf_angle_d1.1723464
X-RAY DIFFRACTIONf_chiral_restr0.082364
X-RAY DIFFRACTIONf_plane_restr0.006446
X-RAY DIFFRACTIONf_dihedral_angle_d14.358981
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.28820.34591100.2992503261397
2.2882-2.39230.31951610.27552461262298
2.3923-2.51840.30241250.25372516264198
2.5184-2.67620.29841270.23942524265198
2.6762-2.88270.29491560.22942523267999
2.8827-3.17270.26381660.19312527269399
3.1727-3.63150.24681230.17512575269899
3.6315-4.57410.20631440.157326182762100
4.5741-38.37940.22641250.17722724284999

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