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- PDB-1i57: CRYSTAL STRUCTURE OF APO HUMAN PTP1B (C215S) MUTANT -

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Entry
Database: PDB / ID: 1i57
TitleCRYSTAL STRUCTURE OF APO HUMAN PTP1B (C215S) MUTANT
ComponentsPHOSPHO-TYROSINE PHOSPHATASE 1B
KeywordsHYDROLASE / Substrate-trapping mutant / conformational change / WPD loop / phosphate-binding loop
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
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsScapin, G. / Patel, S. / Patel, V. / Kennedy, B. / Asante-Appiah, E.
Citation
Journal: Protein Sci. / Year: 2001
Title: The structure of apo protein-tyrosine phosphatase 1B C215S mutant: more than just an S --> O change.
Authors: Scapin, G. / Patel, S. / Patel, V. / Kennedy, B. / Asante-Appiah, E.
#1: Journal: Biochemistry / Year: 1997
Title: The Single Sulfur to Oxygen Substitution in the Active Site Nucleofile of the Yersinia Protein-tyrosine Phosphatase Leads to Substantial Structural and Functional Perturbations
Authors: Zhang, Z.Y. / Wu, L.
#2: Journal: Biochemistry / Year: 1997
Title: Rapid Loop Dynamics of Yersinia Protein-Tyrosine Phosphatase
Authors: Juszczak, L.J. / Zhang, Z.Y. / Wu, L. / Gottfried, D.S. / Eads, D.D.
#3: Journal: Biochemistry / Year: 1998
Title: Conformational and Dynamic Changes of Yersinia Protein Tyrosine Phosphatase Induced by Ligand Binding and Active Site Mutation and Revealed by H/D Exchange and Electrospray Ionization Fourier ...Title: Conformational and Dynamic Changes of Yersinia Protein Tyrosine Phosphatase Induced by Ligand Binding and Active Site Mutation and Revealed by H/D Exchange and Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Authors: Wang, F. / Li, W. / Emmett, M.R. / Hendrickson, C.L. / Marshall, A.G. / Zhang, Y.L. / Wu, L. / Zhang, Z.Y.
#4: Journal: J.Biol.Chem. / Year: 2000
Title: Thermodynamic Study of Ligand Binding to Protein-tyrosine Phosphatase 1B and its Substrate-trapping Mutants.
Authors: Zhang, Y.L. / Yao, Z.J. / Sarmiento, M. / Wu, L. / Burke, T.R. / Zhang, Z.Y.
History
DepositionFeb 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE FIRST 12 RESIDUES ARE THE KODAK FLAG USED FOR PURIFICATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHO-TYROSINE PHOSPHATASE 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4247
Polymers36,2221
Non-polymers2026
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.381, 87.381, 95.942
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 PHOSPHO-TYROSINE PHOSPHATASE 1B / PTP-1B / PROTEIN-TYROSINE PHOSPHATASE / NON-RECEPTOR TYPE 1 / PROTEIN-TYROSINE PHOSPHATASE 1B


Mass: 36222.109 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN (1-298) / Mutation: C215S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTN1_HUMAN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 284 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350, Hepes, Magnesium Chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 284K
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMHEPES1drop
350 mM1dropNaCl
41 mMEDTA1drop
55 mMDMH1drop
613-16 %PEG33501reservoir
7100 mMHEPES1reservoir
8200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 25206 / Num. obs: 25181 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.097 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4136 / Rsym value: 0.0486 / % possible all: 100
Reflection
*PLUS
Num. measured all: 259144
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 4136 / Num. measured obs: 43394

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PTY

1pty


Resolution: 2.1→20 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: MD:Torsion annealing, constant, starting T=2000 Anisotropic B-correction resolution 6-2.1 Ang. Bulk solvent (mask) density level 0.360 e/A^3, B-factor = 58.95 A^2
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1180 5 %RANDOM
Rwork0.195 ---
obs0.21 23604 93.8 %-
all-25161 --
Solvent computationSolvent model: mask / Bsol: 59 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.431 Å2-2.278 Å20 Å2
2--1.431 Å20 Å2
3----2.862 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 6 250 2566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.59
LS refinement shellResolution: 2.1→2.2 Å
RfactorNum. reflection% reflection
Rfree0.432 157 -
Rwork0.309 2642 -
obs-2642 67.7 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.21 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.3 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.432 / Rfactor Rwork: 0.309

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