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- PDB-4hjp: SHP-1 catalytic domain WPD loop open -

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Basic information

Entry
Database: PDB / ID: 4hjp
TitleSHP-1 catalytic domain WPD loop open
ComponentsTyrosine-protein phosphatase non-receptor type 6
KeywordsHYDROLASE / Phosphatase domain
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 / phosphorylation-dependent protein binding / negative regulation of inflammatory response to wounding / 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 / phosphorylation-dependent protein binding / negative regulation of inflammatory response to wounding / 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 / Regulation of KIT signaling / Signaling by ALK / Platelet sensitization by LDL / negative regulation of MAPK cascade / 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 / Interleukin receptor SHC signaling / hematopoietic progenitor cell differentiation / T cell proliferation / Regulation of IFNG signaling / Growth hormone receptor signaling / negative regulation of T cell proliferation / GPVI-mediated activation cascade / T cell costimulation / cell adhesion molecule binding / phosphotyrosine residue binding / SH2 domain binding / protein dephosphorylation / regulation of ERK1 and ERK2 cascade / protein-tyrosine-phosphatase / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / platelet aggregation / SH3 domain binding / cytokine-mediated signaling pathway / 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 / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / 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 / 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-6, -11 / 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 / 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: 1.3994 Å
AuthorsAlicea-Velazquez, N.L. / Boggon, T.J.
CitationJournal: Protein Pept.Lett. / Year: 2013
Title: SHP Family Protein Tyrosine Phosphatases Adopt Canonical Active-Site Conformations in the Apo and Phosphate-Bound States.
Authors: Alicea-Velazquez, N.L. / Boggon, T.J.
History
DepositionOct 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)32,9341
Polymers32,9341
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.482, 57.388, 110.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-842-

HOH

DetailsTHE AUTHORS REPORT THAT THE PROTEIN ELUTES AS MONOMER FROM SIZE EXCLUSION CHROMATOGRAPHY

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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: 32934.180 Da / Num. of mol.: 1 / Fragment: Phosphatase domain (UNP Residues 242-528)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCP, PTP1C, PTPN6, SHP-1 (PTPN6) / Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.0 M tri-sodium citrate, 2-4% 1-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2011 / Details: mirrors
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.399→50 Å / Num. all: 58099 / Num. obs: 57587 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 29.763
Reflection shellResolution: 1.399→1.45 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.182 / Num. unique all: 5597 / Rsym value: 0.756 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FPR

1fpr


Resolution: 1.3994→42.076 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2910 5.05 %Random
Rwork0.1641 ---
obs0.1652 57594 99.22 %-
all-57594 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.204 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5201 Å20 Å2-0 Å2
2--1.4543 Å20 Å2
3----1.9745 Å2
Refinement stepCycle: LAST / Resolution: 1.3994→42.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 0 280 2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012492
X-RAY DIFFRACTIONf_angle_d1.3453414
X-RAY DIFFRACTIONf_dihedral_angle_d14.582992
X-RAY DIFFRACTIONf_chiral_restr0.089367
X-RAY DIFFRACTIONf_plane_restr0.007454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3994-1.42240.52281360.47492477X-RAY DIFFRACTION96
1.4224-1.44690.43011300.37982518X-RAY DIFFRACTION98
1.4469-1.47320.34821370.33432555X-RAY DIFFRACTION98
1.4732-1.50150.27811440.2412525X-RAY DIFFRACTION99
1.5015-1.53220.2351410.21172533X-RAY DIFFRACTION99
1.5322-1.56550.2481550.18342560X-RAY DIFFRACTION99
1.5655-1.60190.22171330.17532573X-RAY DIFFRACTION99
1.6019-1.6420.18781330.16432597X-RAY DIFFRACTION99
1.642-1.68640.21391510.15712556X-RAY DIFFRACTION99
1.6864-1.7360.18251330.14442607X-RAY DIFFRACTION100
1.736-1.7920.16921360.13372594X-RAY DIFFRACTION100
1.792-1.85610.15441240.13032597X-RAY DIFFRACTION100
1.8561-1.93040.18471460.12772601X-RAY DIFFRACTION100
1.9304-2.01830.1721530.14492597X-RAY DIFFRACTION100
2.0183-2.12470.17921350.14042619X-RAY DIFFRACTION100
2.1247-2.25780.17211350.14872645X-RAY DIFFRACTION100
2.2578-2.43210.19061240.14552647X-RAY DIFFRACTION100
2.4321-2.67680.18041310.16182667X-RAY DIFFRACTION100
2.6768-3.0640.18681310.17042686X-RAY DIFFRACTION100
3.064-3.85990.14861480.15492703X-RAY DIFFRACTION100
3.8599-42.09460.18331540.16872827X-RAY DIFFRACTION100

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