+Open data
-Basic information
Entry | Database: PDB / ID: 3olr | ||||||
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Title | PTPN22 in complex with consensus phospho-tyrosine peptide 1 | ||||||
Components |
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Keywords | HYDROLASE / PTPN22 / LYP / phosphatase | ||||||
Function / homology | Function and homology information 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 / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 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 / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / 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 / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / T cell differentiation / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / protein dephosphorylation / negative regulation of autophagy / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Yu, X. / Sun, J.-P. / Zhang, S. / Zhang, Z.-Y. | ||||||
Citation | Journal: To be Published Title: Structure basis of LYP substrate specificity revealed by reverse alanine screening and crystallography Authors: Yu, X. / Sun, J.P. / Chen, M. / Zhang, S. / Wang, L. / Imasaki, T. / Takagi, Y. / Zhang, Z.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3olr.cif.gz | 257.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3olr.ent.gz | 217.1 KB | Display | PDB format |
PDBx/mmJSON format | 3olr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/3olr ftp://data.pdbj.org/pub/pdb/validation_reports/ol/3olr | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 36743.066 Da / Num. of mol.: 4 / Fragment: UNP residues 1-294 / Mutation: C227S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN22, PTPN8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase #2: Protein/peptide | Mass: 1246.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence is derived from a peptide screen #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.1M Tris-Hcl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Dec 17, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→80 Å / Num. all: 41830 / Num. obs: 40826 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 79.23 Å2 / Biso mean: 31.5333 Å2 / Biso min: 6.94 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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Xplor file |
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