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- PDB-4gry: Crystal structure of SHP1 catalytic domain with SO4 -

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Basic information

Entry
Database: PDB / ID: 4gry
TitleCrystal structure of SHP1 catalytic domain with SO4
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 / 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 / negative regulation of T cell receptor signaling pathway / megakaryocyte development / 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 / regulation of type I interferon-mediated signaling pathway / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / non-membrane spanning protein tyrosine phosphatase activity / 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 / Nuclear events stimulated by ALK signaling in cancer / Regulation of IFNG signaling / T cell proliferation / negative regulation of T cell proliferation / Growth hormone receptor signaling / cell adhesion molecule binding / GPVI-mediated activation cascade / 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 / cytokine-mediated signaling pathway / platelet aggregation / 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 / 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 / cytoplasm / cytosol
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: 1.6998 Å
AuthorsAlicea-Velazquez, N.L. / Jakoncic, J. / Boggon, T.J.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Structure-guided studies of the SHP-1/JAK1 interaction provide new insights into phosphatase catalytic domain substrate recognition.
Authors: Alicea-Velazquez, N.L. / Jakoncic, J. / Boggon, T.J.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3May 8, 2013Group: Structure summary
Revision 1.4Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,1103
Polymers32,9181
Non-polymers1922
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.644, 57.281, 110.877
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-898-

HOH

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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: 32918.117 Da / Num. of mol.: 1 / Fragment: Phosphatase domain UNP Residues 242-528 / Mutation: C453S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCP, PTP1C, PTPN6, SHP-1 / Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 44.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 1.5 M ammonium sulfate, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 21, 2011 / Details: mirrors
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.6998→30 Å / Num. all: 29703 / Num. obs: 29703 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rsym value: 0.058 / Net I/σ(I): 19.545
Reflection shellResolution: 1.6998→1.76 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.53 / Rsym value: 0.4 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FPR

1fpr


Resolution: 1.6998→25.676 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1498 5.07 %random
Rwork0.1899 ---
obs0.192 29569 90.2 %-
all-29569 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.215 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5164 Å20 Å20 Å2
2--0.3259 Å2-0 Å2
3---4.1905 Å2
Refinement stepCycle: LAST / Resolution: 1.6998→25.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 10 228 2427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062290
X-RAY DIFFRACTIONf_angle_d0.9943113
X-RAY DIFFRACTIONf_dihedral_angle_d13.686868
X-RAY DIFFRACTIONf_chiral_restr0.073336
X-RAY DIFFRACTIONf_plane_restr0.004405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6998-1.75470.28541380.24882693X-RAY DIFFRACTION97
1.7547-1.81730.30461570.20972722X-RAY DIFFRACTION98
1.8173-1.89010.30651510.24052706X-RAY DIFFRACTION98
1.8901-1.97610.37731190.30182162X-RAY DIFFRACTION77
1.9761-2.08020.23761530.18452759X-RAY DIFFRACTION100
2.0802-2.21050.21931390.17952780X-RAY DIFFRACTION99
2.2105-2.3810.227810.17591501X-RAY DIFFRACTION53
2.381-2.62050.23691320.17212837X-RAY DIFFRACTION100
2.6205-2.99910.23691540.18412844X-RAY DIFFRACTION100
2.9991-3.77670.18041200.17592292X-RAY DIFFRACTION80
3.7767-25.6790.20571540.18182775X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0296-0.2363-0.35642.16223.17814.6809-0.0457-0.0031-0.02490.5364-0.08060.09550.7385-0.29490.1410.2393-0.0511-0.01650.2890.02760.237-13.79111.04997.5585
22.2608-0.01920.00551.44850.39571.341-0.0180.08410.09580.02880.0321-0.0041-0.0220.0002-0.00430.10420.0045-0.00810.0697-0.00910.0659-0.011915.871921.022
32.6753-0.461-0.01042.29780.48071.9675-0.02330.08610.0580.0420.1919-0.2107-0.06020.2183-0.1530.0751-0.0027-0.0330.0979-0.01760.140211.494612.313120.119
42.8232-0.25240.35151.0963-0.20591.37120.04020.2883-0.3244-0.056-0.019-0.09440.23920.1222-0.04050.19120.0044-0.02570.1681-0.06160.12548.7511-4.066511.6888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 243:273)
2X-RAY DIFFRACTION2chain 'A' and (resseq 274:386)
3X-RAY DIFFRACTION3chain 'A' and (resseq 387:457)
4X-RAY DIFFRACTION4chain 'A' and (resseq 458:525)

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