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- PDB-7s4f: Protein Tyrosine Phosphatase 1B - F182Q mutant bound with Hepes -

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Basic information

Entry
Database: PDB / ID: 7s4f
TitleProtein Tyrosine Phosphatase 1B - F182Q mutant bound with Hepes
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsSTRUCTURAL PROTEIN / HYDROLASE / P-loop / WPD-loops / Hepes / 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 / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome ...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 / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / mitochondrial crista / 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 JUN kinase activity / positive regulation of systemic arterial blood pressure / negative regulation of MAP kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNA/IFNB signaling / regulation of proteolysis / cellular response to angiotensin / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of cell-substrate adhesion / cellular response to unfolded protein / regulation of signal transduction / Regulation of IFNG signaling / negative regulation of signal transduction / Growth hormone receptor signaling / positive regulation of cardiac muscle cell apoptotic process / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein dephosphorylation / endoplasmic reticulum unfolded protein response / MECP2 regulates neuronal receptors and channels / ephrin receptor binding / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / cellular response to fibroblast growth factor stimulus / Integrin signaling / protein-tyrosine-phosphatase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to nitric oxide / 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 / insulin receptor binding / response to nutrient levels / Negative regulation of MET activity / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / 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 / cytoplasm / cytosol
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 profile. / Tyrosine-specific protein phosphatases domain / 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBrandao, T.A.S. / Hengge, A.C. / Johnson, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM47297 United States
CitationJournal: Chem Sci / Year: 2022
Title: Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases.
Authors: Shen, R. / Crean, R.M. / Olsen, K.J. / Corbella, M. / Calixto, A.R. / Richan, T. / Brandao, T.A.S. / Berry, R.D. / Tolman, A. / Loria, J.P. / Johnson, S.J. / Kamerlin, S.C.L. / Hengge, A.C.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: 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 25, 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)35,1485
Polymers34,7021
Non-polymers4474
Water5,675315
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)88.316, 88.316, 103.895
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: 34701.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: organ, tissue, cell / Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Plasmid: pEt-19b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2uL of protein solution (12 mg/mL PTP1B F182Q in 10 mM Tris pH 7.5, 25 mM NaCl, 0.2 mM EDTA and 3 mM DTT), 0.5 uL sucrose 30% (w/v) and 3 uL of precipitant solution (0.1 M Hepes pH 7.5, 0.2 ...Details: 2uL of protein solution (12 mg/mL PTP1B F182Q in 10 mM Tris pH 7.5, 25 mM NaCl, 0.2 mM EDTA and 3 mM DTT), 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 well solution was 500 uL of precipitant solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.55 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 20, 2007
RadiationMonochromator: Osmic Blue Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 53917 / % possible obs: 94.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 0.701 / Rmerge(I) obs: 0.048 / Χ2: 1.027 / Net I/σ(I): 24.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.65-1.7130.49137731.007167.3
1.71-1.783.80.35148361.067186
1.78-1.865.30.26156001.051199.8
1.86-1.965.50.18556401.0671100
1.96-2.085.50.12556501.0371100
2.08-2.245.60.0956501.0181100
2.24-2.465.60.06956721.041199.9
2.46-2.825.70.05756690.969199.5
2.82-3.555.80.04357100.949199
3.55-505.80.03357171.076196

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I80

3i80


Resolution: 1.65→22.887 Å / FOM work R set: 0.8748 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 2719 5.05 %
Rwork0.1798 51168 -
obs0.181 53887 94.88 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.244 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 151.31 Å2 / Biso mean: 33.31 Å2 / Biso min: 12.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.65→22.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 28 315 2775
Biso mean--50.4 42.9 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062532
X-RAY DIFFRACTIONf_angle_d1.0343415
X-RAY DIFFRACTIONf_chiral_restr0.075360
X-RAY DIFFRACTIONf_plane_restr0.004439
X-RAY DIFFRACTIONf_dihedral_angle_d14.125979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.6878179963
1.68-1.71230.36051020.3147202172
1.7123-1.74730.31231270.2752230982
1.7473-1.78520.28061520.2528258493
1.7852-1.82670.24461420.21642837100
1.8267-1.87240.22511580.20742800100
1.8724-1.9230.19571410.19132829100
1.923-1.97960.21861480.18572817100
1.9796-2.04340.20011550.18212803100
2.0434-2.11640.21061740.18482778100
2.1164-2.20110.20911560.17232854100
2.2011-2.30120.19071420.17932815100
2.3012-2.42240.20731650.17712795100
2.4224-2.57390.19161290.18152873100
2.5739-2.77240.21971490.18182839100
2.7724-3.05080.22091550.1846283899
3.0508-3.49090.20091580.1741282999
3.4909-4.39310.18411470.1476284298
4.3931-22.8870.17651410.1744290696
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0194-0.0101-0.01160.1310.08560.1140.0148-0.2390.31070.08630.42040.24480.0099-1.1565-0.4680.2704-0.0157-0.08390.55390.01970.461719.0441-17.783211.9286
21.3551-0.0346-0.29971.9082-0.52761.28460.05830.40560.2172-0.09280.17390.0948-0.2787-0.1584-0.2430.23060.1123-0.0390.29090.06270.203529.3941-5.62726.2889
30.5072-0.3491-0.0650.7176-0.38360.52730.06920.06260.2874-0.081-0.0107-0.2581-0.36120.0081-0.06150.26670.02380.03620.10780.01120.236452.7006-2.12479.0795
41.1572-0.4124-0.33411.3298-0.27660.32920.03010.04930.05770.0714-0.0586-0.1338-0.0145-0.01650.03380.18680.04380.00440.1135-0.00940.12450.9356-15.140214.1672
51.1434-0.6777-0.31731.2906-0.4230.7832-0.0437-0.09150.2391-0.2694-0.05790.12260.20590.27320.08980.17050.093-0.01540.15110.03010.235365.4263-23.501515.1561
62.56360.34640.21410.0787-0.00340.5728-0.41750.0001-0.4532-0.29190.23030.06430.1053-0.02660.18950.31420.0529-0.00240.14020.0110.270952.0506-30.742217.2469
72.22720.1379-0.34730.74240.11450.18-0.136-0.0243-0.1414-0.02090.08310.00670.0916-0.02280.06010.26620.05020.00150.1410.01210.145247.4969-24.037617.8066
80.58850.1569-0.06960.3879-0.36990.3915-0.050.02330.1530.05860.05040.0237-0.127-0.0252-0.00690.2160.05730.01020.1251-0.03450.137246.0668-16.412618.0646
91.4650.59420.11071.0956-0.58980.47280.0729-0.00420.10330.1211-0.00190.131-0.0568-0.0944-0.07160.19940.04720.02680.1456-0.00070.146632.3666-13.32517.654
102.16140.6466-0.91040.26820.01292.5048-0.1696-0.0538-0.56830.333-0.015-0.07070.5431-0.13480.18630.3289-0.0296-0.00620.1704-0.01640.259631.5109-30.190320.5911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:16)A1 - 16
2X-RAY DIFFRACTION2(chain A and resid 17:29)A17 - 29
3X-RAY DIFFRACTION3(chain A and resid 30:66)A30 - 66
4X-RAY DIFFRACTION4(chain A and resid 67:125)A67 - 125
5X-RAY DIFFRACTION5(chain A and resid 126:146)A126 - 146
6X-RAY DIFFRACTION6(chain A and resid 147:160)A147 - 160
7X-RAY DIFFRACTION7(chain A and resid 161:202)A161 - 202
8X-RAY DIFFRACTION8(chain A and resid 203:223)A203 - 223
9X-RAY DIFFRACTION9(chain A and resid 224:268)A224 - 268
10X-RAY DIFFRACTION10(chain A and resid 269:298)A269 - 298

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