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- PDB-7fqr: PanDDA analysis group deposition -- Crystal structure of PTP1B in... -

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Basic information

Entry
Database: PDB / ID: 7fqr
TitlePanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000666a
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PanDDA / Diamond i24 fragment screening / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multiconformer
Function / homology
Function and homology information


regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / 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 / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / positive regulation of protein tyrosine kinase activity / 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 / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / Growth hormone receptor signaling / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / protein phosphatase 2A binding / negative regulation of MAP kinase activity / protein tyrosine phosphatase activity / 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 / Tyrosine-specific protein phosphatases domain ...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
Chem-JPD / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMehlman, T. / Biel, J. / Azeem, S.M. / Nelson, E.R. / Hossain, S. / Dunnett, L.E. / Paterson, N.G. / Douangamath, A. / Talon, R. / Axford, D. ...Mehlman, T. / Biel, J. / Azeem, S.M. / Nelson, E.R. / Hossain, S. / Dunnett, L.E. / Paterson, N.G. / Douangamath, A. / Talon, R. / Axford, D. / Orins, H. / von Delft, F. / Keedy, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
U.S. Department of Education Graduate Assistance in Areas of National Need (GAANN)PA200A150068 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133769 United States
CitationJournal: Elife / Year: 2023
Title: Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B.
Authors: Skaist Mehlman, T. / Biel, J.T. / Azeem, S.M. / Nelson, E.R. / Hossain, S. / Dunnett, L. / Paterson, N.G. / Douangamath, A. / Talon, R. / Axford, D. / Orins, H. / von Delft, F. / Keedy, D.A.
History
DepositionOct 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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)37,7113
Polymers37,3461
Non-polymers3652
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.570, 89.570, 106.440
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 / Mutation: C32S/C92V
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-JPD / methyl (1S,3S,4R)-4-hydroxy-3-[(1S)-1-hydroxypropyl]-2-azabicyclo[2.2.2]octane-2-carboxylate


Mass: 243.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→62.69 Å / Num. obs: 39413 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.942 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.113 / Χ2: 0.973 / Net I/σ(I): 12 / Num. measured all: 384144
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.951.281.1624900286928690.5171.362100
1.95-21.1081.5626703279527950.6471.171100
2-2.060.9122.1827722272827280.7570.961100
2.06-2.120.7792.6826048266926690.810.823100
2.12-2.190.6213.6625908257125710.9030.655100
2.19-2.270.5024.5124195248124810.9410.531100
2.27-2.360.4235.3222866244424440.9470.449100
2.36-2.450.3326.9222157229522950.9680.351100
2.45-2.560.286821180222722270.9750.303100
2.56-2.690.23710.1421805213421340.9850.249100
2.69-2.830.19612.1820608203420340.9880.206100
2.83-30.15514.7219029193419340.9930.163100
3-3.210.1218.4118225182518250.9960.127100
3.21-3.470.09223.717597169716970.9970.096100
3.47-3.80.07229.1615731155915590.9970.076100
3.8-4.250.05933.6514094143614360.9980.062100
4.25-4.910.04938.3912343126412640.9990.052100
4.91-6.010.0536.910694109510950.9990.053100
6.01-8.50.04936.6778418458450.9990.052100
8.50.0443.7744985145110.9970.04299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.83 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.956 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 1553 3.9 %RANDOM
Rwork0.1759 ---
obs0.177 37860 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.64 Å2 / Biso mean: 42.375 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.9→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 58 174 2529
Biso mean--63.94 54.11 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0386402
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153520
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6565269
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5998234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54622.19210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44415706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8151526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024650
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02942
X-RAY DIFFRACTIONr_mcbond_it3.9083.9553200
X-RAY DIFFRACTIONr_mcbond_other3.8883.9333129
X-RAY DIFFRACTIONr_mcangle_it4.4115.8442401
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 112 -
Rwork0.335 2751 -
all-2863 -
obs--99.79 %

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