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- PDB-6xe8: Crystal Structure of the PTP1B YopH WPD loop Chimera 3 apo form -

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Basic information

Entry
Database: PDB / ID: 6xe8
TitleCrystal Structure of the PTP1B YopH WPD loop Chimera 3 apo form
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PTP1B / tyrosine phosphatase / WPD loop
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
BENZAMIDINE / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.952 Å
AuthorsOlsen, K.J. / Shen, R. / Johnson, S.J. / Hengge, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112781 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
DepositionJun 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: 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

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6225
Polymers37,3321
Non-polymers2914
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.955, 87.955, 102.606
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: 37331.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.17 Å3/Da / Density % sol: 59.92 % / Description: Rods
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: tris hydrochloride pH 8.5, magnesium acetate tetrahydrate, PEG 8000 and benzamidine
PH range: 7.8-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 33776 / % possible obs: 99.8 % / Redundancy: 17.9 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Χ2: 1.011 / Net I/σ(I): 10.7 / Num. measured all: 604329
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.0211.20.75232310.8150.220.7861.07597.8
2.02-2.114.50.60333540.9040.1590.6251.082100
2.1-2.218.70.40733300.9750.0960.4191100
2.2-2.3119.30.31233680.9870.0730.3211.031100
2.31-2.4618.60.20933560.9920.0490.2140.997100
2.46-2.6518.90.14433590.9960.0340.1480.983100
2.65-2.9119.90.10233700.9980.0230.1051.011100
2.91-3.3318.70.06633950.9990.0160.0671.01299.9
3.33-4.220.20.043343610.010.0440.933100
4.2-5018.40.028357710.0070.0291.03899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.1 Å43.98 Å
Translation6.1 Å43.98 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.1phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QKP

3qkp


Resolution: 1.952→43.977 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 1708 5.06 %
Rwork0.1632 32032 -
obs0.1643 33740 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.68 Å2 / Biso mean: 49.8204 Å2 / Biso min: 24.73 Å2
Refinement stepCycle: final / Resolution: 1.952→43.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 19 142 2561
Biso mean--59.34 51.55 -
Num. residues----296
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9523-2.00980.27571330.2314256697
2.0098-2.07460.22771530.21162605100
2.0746-2.14880.20791480.18292637100
2.1488-2.23480.18311460.16542642100
2.2348-2.33650.20791410.17042659100
2.3365-2.45970.21021490.17242651100
2.4597-2.61380.20631230.17552659100
2.6138-2.81560.2331400.18112680100
2.8156-3.09890.2141500.18042654100
3.0989-3.54710.20381490.16782711100
3.5471-4.46830.16231400.13682728100
4.4683-43.9770.13891360.15212840100
Refinement TLS params.Method: refined / Origin x: -44.1309 Å / Origin y: 16.8458 Å / Origin z: 14.762 Å
111213212223313233
T0.3285 Å20.028 Å20.0011 Å2-0.1959 Å20.0324 Å2--0.2372 Å2
L2.5608 °2-0.6751 °20.4693 °2-3.5761 °20.4021 °2--2.0969 °2
S0.0316 Å °0.039 Å °0.0763 Å °-0.0075 Å °-0.0107 Å °-0.1909 Å °-0.1236 Å °0.1704 Å °-0.0267 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 298
2X-RAY DIFFRACTION1allB1 - 4
3X-RAY DIFFRACTION1allC1 - 143

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