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- PDB-7gt5: PanDDA Analysis group deposition -- Crystal structure of PTP1B in... -

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Basic information

Entry
Database: PDB / ID: 7gt5
TitlePanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000529a
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PanDDA / Diamond I04-1 fragment screening / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / 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 / 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, 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
Chem-A1ABK / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsMehlman, T. / Ginn, H.M. / Keedy, D.A.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133769 United States
Helmholtz AssociationVH-NG-19-02 Germany
CitationJournal: Biorxiv / Year: 2024
Title: An expanded view of ligandability in the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data.
Authors: Mehlman, T.S. / Ginn, H.M. / Keedy, D.A.
History
DepositionJan 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: 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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,0664
Polymers37,3461
Non-polymers7213
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.945, 89.945, 106.709
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


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-A1ABK / methyl [(3R,4S)-3-ethyl-4-hydroxy-1,1-dioxo-3,4-dihydro-1lambda~6~,2-benzothiazin-2(1H)-yl]acetate


Mass: 299.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17NO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.61→62.915 Å / Num. obs: 124267 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.841 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.067 / Χ2: 1.067 / Net I/σ(I): 12.38 / Num. measured all: 596726
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.61-1.710.8991.087288520125199880.5121.05699.3
1.71-1.830.4962.328014518910188790.8350.56899.8
1.83-1.980.2475.128701917646176450.9620.276100
1.98-2.160.13310.078626316185161850.9880.148100
2.16-2.420.08715.197501914662146580.9930.096100
2.42-2.790.06621.326950912927129270.9960.073100
2.79-3.420.05327.075703810899108960.9970.059100
3.42-4.830.04931.943870844584400.9970.05599.9
4.83-62.9150.04833.7324978465546490.9960.05499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→44.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.063 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 2550 3.9 %RANDOM
Rwork0.2002 ---
obs0.2015 62116 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.45 Å2 / Biso mean: 37.549 Å2 / Biso min: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.22 Å20 Å2
2--0.43 Å20 Å2
3----1.4 Å2
Refinement stepCycle: final / Resolution: 1.61→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 94 230 2641
Biso mean--50.44 46.3 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0284093
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162812
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.6654108
X-RAY DIFFRACTIONr_angle_other_deg1.371.6066521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64621.963163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06915545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3031523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023465
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02709
X-RAY DIFFRACTIONr_mcbond_it3.0743.6852019
X-RAY DIFFRACTIONr_mcbond_other2.9753.6711963
X-RAY DIFFRACTIONr_mcangle_it4.2845.3151819
LS refinement shellResolution: 1.613→1.655 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 189 -
Rwork0.409 4531 -
all-4720 -
obs--99.58 %

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