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- PDB-1gwz: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE PROTEIN TYROSINE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gwz | ||||||
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Title | CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE PROTEIN TYROSINE PHOSPHATASE SHP-1 | ||||||
![]() | SHP-1 | ||||||
![]() | HYDROLASE / PROTEIN TYROSINE PHOSPHATASE / CATALYTIC DOMAIN / WPD LOOP / SH2 DOMAIN | ||||||
Function / homology | ![]() 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 / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol ...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 / 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 / natural killer cell mediated cytotoxicity / 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 / 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 / negative regulation of T cell proliferation / T cell proliferation / Growth hormone receptor signaling / GPVI-mediated activation cascade / cell adhesion molecule binding / T cell costimulation / phosphotyrosine residue binding / protein dephosphorylation / SH2 domain binding / protein-tyrosine-phosphatase / negative regulation of angiogenesis / 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 / 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 / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yang, J. / Liang, X. / Niu, T. / Meng, W. / Zhao, Z. / Zhou, G.W. | ||||||
![]() | ![]() Title: Crystal structure of the catalytic domain of protein-tyrosine phosphatase SHP-1. Authors: Yang, J. / Liang, X. / Niu, T. / Meng, W. / Zhao, Z. / Zhou, G.W. #1: ![]() Title: Expression, Purification, and Crystallization of the Catalytic Domain of Protein Tyrosine Phosphatase Shp-1 Authors: Liang, X. / Meng, W. / Niu, T. / Zhao, Z. / Zhou, G.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67 KB | Display | ![]() |
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PDB format | ![]() | 48.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34289.605 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.79 % | |||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 85 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 8779 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.082 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.5→2.57 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.313 / % possible all: 71.8 |
Reflection | *PLUS Rmerge(I) obs: 0.082 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PTP-1B Resolution: 2.5→6 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Refine analyze | Luzzati coordinate error free: 0.3 Å / Luzzati sigma a free: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.6 Å / Total num. of bins used: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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