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- PDB-5qdp: PanDDA analysis group deposition -- Crystal structure of PTP1B in... -

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Basic information

Entry
Database: PDB / ID: 5qdp
TitlePanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000207a
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PanDDA / SGC - Diamond I04-1 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 / negative regulation of MAP kinase activity / protein-tyrosine-phosphatase / protein phosphatase 2A binding / 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 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, 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
N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.744 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.
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
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
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 / _entity.formula_weight
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)37,6373
Polymers37,3461
Non-polymers2912
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint2 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.552, 89.552, 106.189
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 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-JGA / N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea


Mass: 169.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O2
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
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, 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 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.74→62.63 Å / Num. obs: 97114 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.071 / Χ2: 1.256 / Net I/σ(I): 14.29 / Num. measured all: 503313
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.74-1.850.9881.398083715726157190.51.101100
1.85-1.980.5582.57349314756147540.7870.625100
1.98-2.140.3144.697412313816138160.9340.348100
2.14-2.340.1818.266646512590125900.9780.201100
2.34-2.610.11712.725833111420114180.9910.13100
2.61-3.020.07320.915488110110101100.9960.081100
3.02-3.690.04233.6742238849384900.9980.047100
3.69-5.220.0349.6734388659565930.9990.033100
5.22-62.630.02452.44185573628362410.02799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.744→44.776 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 1995 3.94 %
Rwork0.1798 48667 -
obs0.181 50662 99.99 %
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.07 Å2 / Biso mean: 37.3757 Å2 / Biso min: 12.18 Å2
Refinement stepCycle: final / Resolution: 1.744→44.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 66 264 2635
Biso mean--60.39 46.41 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0246063
X-RAY DIFFRACTIONf_angle_d1.9578366
X-RAY DIFFRACTIONf_chiral_restr0.128826
X-RAY DIFFRACTIONf_plane_restr0.011192
X-RAY DIFFRACTIONf_dihedral_angle_d18.8522537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7439-1.78750.32261430.294334383581
1.7875-1.83590.25521360.262434153551
1.8359-1.88990.24281410.227334523593
1.8899-1.95090.2651390.20534463585
1.9509-2.02060.25161450.204534283573
2.0206-2.10150.24891390.198134453584
2.1015-2.19720.23281420.182734513593
2.1972-2.3130.21041430.172234723615
2.313-2.45790.19571440.166334293573
2.4579-2.64770.17531450.166834913636
2.6477-2.91410.22091430.169834753618
2.9141-3.33560.18981420.173535133655
3.3356-4.2020.19791440.165335373681
4.202-44.79070.21231490.178636753824

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