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- PDB-3h2x: Crystal Structure of The Human Lymphoid Tyrosine Phosphatase Cata... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h2x | ||||||
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Title | Crystal Structure of The Human Lymphoid Tyrosine Phosphatase Catalytic Domain | ||||||
![]() | Tyrosine-protein phosphatase non-receptor type 22 | ||||||
![]() | HYDROLASE / SH2-like fold / Alternative splicing / Cytoplasm / Polymorphism / Protein phosphatase / Systemic lupus erythematosus | ||||||
Function / homology | ![]() phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway ...phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / negative regulation of T cell activation / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of interleukin-8 production / negative regulation of JUN kinase activity / negative regulation of T cell receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of CD8-positive, alpha-beta T cell proliferation / regulation of innate immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / phosphatase activity / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / non-membrane spanning protein tyrosine phosphatase activity / T cell differentiation / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / negative regulation of autophagy / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / lipid metabolic process / cytoplasmic side of plasma membrane / autophagy / kinase binding / SH3 domain binding / positive regulation of type II interferon production / T cell receptor signaling pathway / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / negative regulation of gene expression / ubiquitin protein ligase binding / positive regulation of gene expression / perinuclear region of cytoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tsai, S.J. / Sen, U. | ||||||
![]() | ![]() Title: Crystal structure of the human lymphoid tyrosine phosphatase catalytic domain: insights into redox regulation . Authors: Tsai, S.J. / Sen, U. / Zhao, L. / Greenleaf, W.B. / Dasgupta, J. / Fiorillo, E. / Orru, V. / Bottini, N. / Chen, X.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.7 KB | Display | ![]() |
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PDB format | ![]() | 58.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 448.8 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cfvS S: Starting model for refinement |
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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: 35614.891 Da / Num. of mol.: 1 / Fragment: Catalytic Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 2.0 M (NH4)2SO4, 0.1 M MES, 0.2 M Na/KPO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 93.15 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2007 / Details: Confocal |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 16800 / Observed criterion σ(F): 5 / Observed criterion σ(I): 2.2 / Redundancy: 3.6 % |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.4 / % possible all: 92.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 2CFV Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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