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- PDB-6b8e: Multiconformer model of apo WT PTP1B with glycerol at 180 K -

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Basic information

Entry
Database: PDB / ID: 6b8e
TitleMulticonformer model of apo WT PTP1B with glycerol at 180 K
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multitemperature / multiconformer
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 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
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsKeedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / von Delft, F. / Wells, J.A. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2018
Title: An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.
Authors: Keedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / Pearce, N.M. / von Delft, F. / Wells, J.A. / Fraser, J.S.
History
DepositionOct 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)37,8366
Polymers37,3461
Non-polymers4915
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.570, 88.570, 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: 37345.562 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 16% PEG 8000, 2% ethanol, 10% glycerol

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.82→19.18 Å / Num. obs: 42866 / % possible obs: 99.86 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08943 / Rpim(I) all: 0.03359 / Rrim(I) all: 0.09562 / Net I/σ(I): 21.4
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.483 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 4223 / CC1/2: 0.52 / Rpim(I) all: 0.5558 / Rrim(I) all: 1.585 / % possible all: 99.98

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSMarch 1, 2015data reduction
XSCALEMarch 1, 2015data scaling
PHASERphasing
PHENIX1.12refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→19.18 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.72
RfactorNum. reflection% reflection
Rfree0.1997 1688 3.94 %
Rwork0.1708 --
obs0.1719 42860 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.95 Å2 / Biso mean: 33.4582 Å2 / Biso min: 10.39 Å2
Refinement stepCycle: final / Resolution: 1.82→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 96 294 2825
Biso mean--59.67 39.52 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112802
X-RAY DIFFRACTIONf_angle_d1.0153802
X-RAY DIFFRACTIONf_chiral_restr0.059394
X-RAY DIFFRACTIONf_plane_restr0.008498
X-RAY DIFFRACTIONf_dihedral_angle_d12.4821707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.82-1.87360.29351350.280733983533
1.8736-1.9340.29671410.261333963537
1.934-2.0030.24061450.231433633508
2.003-2.08310.241360.209533903526
2.0831-2.17780.23871330.190734213554
2.1778-2.29250.21231430.173933903533
2.2925-2.43580.21121390.164634193558
2.4358-2.62350.21091460.154433973543
2.6235-2.88670.17931430.148534403583
2.8867-3.30270.16061380.144234553593
3.3027-4.15430.17881400.138334923632
4.1543-19.39030.18581490.17936113760

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