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- PDB-3ps5: Crystal structure of the full-length Human Protein Tyrosine Phosp... -

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Basic information

Entry
Database: PDB / ID: 3ps5
TitleCrystal structure of the full-length Human Protein Tyrosine Phosphatase SHP-1
ComponentsTyrosine-protein phosphatase non-receptor type 6
KeywordsHYDROLASE / SIGNALING PROTEIN / SH2 / PTP / Phosphatase
Function / homology
Function and homology information


negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / negative regulation of inflammatory response to wounding / phosphorylation-dependent protein binding / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex ...negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / negative regulation of inflammatory response to wounding / phosphorylation-dependent protein binding / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Costimulation by the CD28 family / Signal regulatory protein family interactions / platelet formation / megakaryocyte development / negative regulation of T cell receptor signaling pathway / negative regulation of MAPK cascade / Regulation of KIT signaling / Signaling by ALK / Platelet sensitization by LDL / regulation of G1/S transition of mitotic cell cycle / PECAM1 interactions / negative regulation of interleukin-6 production / regulation of type I interferon-mediated signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PD-1 signaling / Nuclear events stimulated by ALK signaling in cancer / Interleukin receptor SHC signaling / hematopoietic progenitor cell differentiation / Regulation of IFNG signaling / T cell proliferation / Growth hormone receptor signaling / negative regulation of T cell proliferation / GPVI-mediated activation cascade / cell adhesion molecule binding / T cell costimulation / phosphotyrosine residue binding / SH2 domain binding / protein dephosphorylation / protein-tyrosine-phosphatase / regulation of ERK1 and ERK2 cascade / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / platelet aggregation / cytokine-mediated signaling pathway / SH3 domain binding / peptidyl-tyrosine phosphorylation / specific granule lumen / Interferon gamma signaling / MAPK cascade / Interferon alpha/beta signaling / cell-cell junction / tertiary granule lumen / mitotic cell cycle / T cell receptor signaling pathway / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / intracellular signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / Neutrophil degranulation / positive regulation of cell population proliferation / nucleolus / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / 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, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWang, W. / Liu, L. / Song, X. / Mo, Y. / Komma, C. / Bellamy, H.D. / Zhao, Z.J. / Zhou, G.W.
CitationJournal: J.Cell.Biochem. / Year: 2011
Title: Crystal structure of human protein tyrosine phosphatase SHP-1 in the open conformation.
Authors: Wang, W. / Liu, L. / Song, X. / Mo, Y. / Komma, C. / Bellamy, H.D. / Zhao, Z.J. / Zhou, G.W.
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1206
Polymers67,6401
Non-polymers4805
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tyrosine-protein phosphatase non-receptor type 6
hetero molecules

A: Tyrosine-protein phosphatase non-receptor type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,24112
Polymers135,2802
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area5230 Å2
ΔGint-162 kcal/mol
Surface area47800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.919, 231.919, 78.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 6 / Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / ...Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / Protein-tyrosine phosphatase SHP-1 / SH-PTP1


Mass: 67639.984 Da / Num. of mol.: 1 / Mutation: C453S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN6, HCP, PTP1C / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5 ul of SHP-1 at 3.5 mg/ml in 25mM Tris-HCl, beta-mercaptoethanol, 1mM EDTA mixed with 2.5 ul of 1.8M ammonium sulfate, 0.1M glycine, 0.1M Tris-HCl, with the addition of 0.5 ul 14mM deoxy ...Details: 2.5 ul of SHP-1 at 3.5 mg/ml in 25mM Tris-HCl, beta-mercaptoethanol, 1mM EDTA mixed with 2.5 ul of 1.8M ammonium sulfate, 0.1M glycine, 0.1M Tris-HCl, with the addition of 0.5 ul 14mM deoxy Big Chap to form the final drop., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.3807 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3807 Å / Relative weight: 1
ReflectionResolution: 3.1→116 Å / Num. obs: 14036 / % possible obs: 99.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.1
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 1.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2B3O

2b3o


Resolution: 3.1→115.96 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.867 / SU B: 21.315 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27576 731 5 %RANDOM
Rwork0.22481 ---
obs0.2272 14036 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 3.1→115.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 25 17 4266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224338
X-RAY DIFFRACTIONr_angle_refined_deg0.8551.9535875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3435528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49424.358218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17515750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3571530
X-RAY DIFFRACTIONr_chiral_restr0.0590.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213329
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 58 -
Rwork0.324 1036 -
obs--100 %

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