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

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Basic information

Entry
Database: PDB / ID: 7fqy
TitlePanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000278a
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


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
Chem-GRY / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 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
Revision 1.2May 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)37,6823
Polymers37,3461
Non-polymers3362
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.610, 89.610, 106.420
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-GRY / ~{N}1-(4,6-dimethylpyrimidin-2-yl)benzene-1,4-diamine


Mass: 214.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 62.76 %
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: 2.13→62.7 Å / Num. obs: 28113 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 45.005 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.145 / Χ2: 0.952 / Net I/σ(I): 7 / Num. measured all: 153827
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.13-2.191.0111.2211831206220600.5251.11299.9
2.19-2.250.831.5811261200920070.6310.91699.9
2.25-2.310.7591.7510605192819260.6450.83999.9
2.31-2.380.6742.0210218188918890.7360.748100
2.38-2.460.5472.6510059182418220.7730.60699.9
2.46-2.550.4852.879481180718030.8360.5499.8
2.55-2.640.4063.569435169316930.8870.45100
2.64-2.750.3314.329019165416530.9250.36899.9
2.75-2.870.2885.068610160015970.9340.3299.8
2.87-3.010.2296.358218152215200.9670.25399.9
3.01-3.180.1927.628058145514540.9680.21299.9
3.18-3.370.159.837752138313820.9820.16699.9
3.37-3.60.11812.127331129812970.9890.1399.9
3.6-3.890.09714.146528121512130.9880.10899.8
3.89-4.260.08216.036179113211310.9930.09199.9
4.26-4.760.06918.045341100510030.9940.07699.8
4.76-5.50.07218.2350069139090.9940.07999.6
5.5-6.740.07516.7740417817800.9950.08399.9
6.74-9.530.0619.331546136110.9960.06799.7
9.530.0521.8117003723630.9960.05697.6

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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: 2.13→36.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.405 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1107 3.9 %RANDOM
Rwork0.163 ---
obs0.1648 27008 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.5 Å2 / Biso mean: 46.049 Å2 / Biso min: 26.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.13→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 49 177 2523
Biso mean--81.7 59.96 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152802
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6434205
X-RAY DIFFRACTIONr_angle_other_deg1.3121.5836528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52622.56168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21715565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6341520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023774
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02766
X-RAY DIFFRACTIONr_mcbond_it3.664.3031835
X-RAY DIFFRACTIONr_mcbond_other3.5454.2811786
X-RAY DIFFRACTIONr_mcangle_it4.9496.4561936
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 82 -
Rwork0.296 1976 -
all-2058 -
obs--99.76 %

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