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- PDB-1nwe: Ptp1B R47C Modified at C47 with N-[4-(2-{2-[3-(2-Bromo-acetylamin... -

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Basic information

Entry
Database: PDB / ID: 1nwe
TitlePtp1B R47C Modified at C47 with N-[4-(2-{2-[3-(2-Bromo-acetylamino)-propionylamino]-3-hydroxy-propionylamino}-ethyl)-phenyl]-oxalamic acid
ComponentsProtein-tyrosine phosphatase, non-receptor type 1
KeywordsHYDROLASE / Acetylation / Phosphorylation / phospatase / phosphotyrosine mimetic
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 / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / 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 / positive regulation of protein tyrosine kinase 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 / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / 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 / cytoplasm / cytosol
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
Chem-FG1 / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsErlanson, D.A. / McDowell, R.S. / He, M.M. / Randal, M. / Simmons, R.L. / Kung, J. / Waight, A. / Hansen, S.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Discovery of a New Phosphotyrosine Mimetic for PTP1B Using Breakaway Tethering
Authors: Erlanson, D.A. / McDowell, R.S. / He, M.M. / Randal, M. / Simmons, R.L. / Kung, J. / Waight, A. / Hansen, S.K.
History
DepositionFeb 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600Heterogen The Br atom of the ligand was displaced during the covalent modification of the protein.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine phosphatase, non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1342
Polymers34,6461
Non-polymers4871
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.052, 88.052, 117.594
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein-tyrosine phosphatase, non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 34646.441 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1-298 / Mutation: C32S, R47C, C92V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1 / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-FG1 / N-[4-(2-{2-[3-(2-BROMO-ACETYLAMINO)-PROPIONYLAMINO]-3-HYDROXY-PROPIONYLAMINO}-ETHYL)-PHENYL]-OXALAMIC ACID


Mass: 487.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23BrN4O7

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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: 3.93 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 8k, HEPES, MgOAc, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 6, 2002 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→15 Å / Num. all: 9867 / Num. obs: 9867 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.187 / Rsym value: 0.187 / Net I/σ(I): 5.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.6 / Num. unique all: 964 / Rsym value: 0.397 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: native PTP-1B

Resolution: 3.1→15 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.808 / SU B: 35.84 / SU ML: 0.581 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30544 447 4.9 %RANDOM
Rwork0.28295 ---
all0.284 8660 --
obs0.28401 8660 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 2.352 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å2-1.3 Å20 Å2
2---2.6 Å20 Å2
3---3.9 Å2
Refinement stepCycle: LAST / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 29 0 2391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212442
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.9553301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5715294
X-RAY DIFFRACTIONr_chiral_restr0.0590.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021865
X-RAY DIFFRACTIONr_nbd_refined0.1980.21098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.217
X-RAY DIFFRACTIONr_mcbond_it0.362.51474
X-RAY DIFFRACTIONr_mcangle_it0.49652373
X-RAY DIFFRACTIONr_scbond_it0.4462.5968
X-RAY DIFFRACTIONr_scangle_it0.6245928
LS refinement shellResolution: 3.1→3.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 40 -
Rwork0.379 592 -
obs-632 94 %
Refinement TLS params.Method: refined / Origin x: 40.1008 Å / Origin y: 46.131 Å / Origin z: 42.4608 Å
111213212223313233
T0.0029 Å2-0.0302 Å2-0.0087 Å2-0.5577 Å2-0.0028 Å2--0.0625 Å2
L7.1211 °2-1.8696 °2-0.5645 °2-3.886 °21.1956 °2--4.0721 °2
S-0.0255 Å °0.6446 Å °0.328 Å °-0.1088 Å °-0.0216 Å °-0.1167 Å °-0.3754 Å °0.1669 Å °0.0471 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2972 - 297
2X-RAY DIFFRACTION1AB10011

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