+Open data
-Basic information
Entry | Database: PDB / ID: 2nz6 | ||||||
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Title | Crystal structure of the PTPRJ inactivating mutant C1239S | ||||||
Components | Receptor-type tyrosine-protein phosphatase eta | ||||||
Keywords | HYDROLASE / HYDROLASE RECEPTOR TYPE TYROSINE PHOSPHATASE J / PTPRJ / GLYCOPROTEIN / PROTEIN PHOSPHATASE / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / negative regulation of epidermal growth factor receptor signaling pathway / platelet-derived growth factor receptor binding / positive regulation of platelet activation / negative regulation of vascular permeability / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding ...positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / negative regulation of epidermal growth factor receptor signaling pathway / platelet-derived growth factor receptor binding / positive regulation of platelet activation / negative regulation of vascular permeability / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / platelet formation / negative regulation of T cell receptor signaling pathway / positive chemotaxis / positive regulation of macrophage chemotaxis / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation / phosphatase activity / positive regulation of focal adhesion assembly / platelet-derived growth factor receptor signaling pathway / immunological synapse / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell adhesion / peptidyl-tyrosine dephosphorylation / vasculogenesis / regulation of cell adhesion / specific granule membrane / positive regulation of phagocytosis / negative regulation of MAP kinase activity / negative regulation of insulin receptor signaling pathway / Negative regulation of FLT3 / positive regulation of calcium-mediated signaling / protein-tyrosine-phosphatase / B cell differentiation / negative regulation of cell migration / protein tyrosine phosphatase activity / ruffle membrane / Negative regulation of MET activity / negative regulation of cell growth / cytokine-mediated signaling pathway / beta-catenin binding / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / blood coagulation / cell-cell junction / glucose homeostasis / heart development / T cell receptor signaling pathway / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cadherin binding / negative regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / cell surface / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ugochukwu, E. / Barr, A. / Savitsky, P. / Pike, A.C.W. / Bunkoczi, G. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. ...Ugochukwu, E. / Barr, A. / Savitsky, P. / Pike, A.C.W. / Bunkoczi, G. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome. Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nz6.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nz6.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 2nz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/2nz6 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/2nz6 | HTTPS FTP |
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-Related structure data
Related structure data | 2ahsC 2b49C 2cfvSC 2cjzC 2gjtC 2h4vC 2i75C 2jjdC 2nlkC 2oc3C 2ooqC 2p6xC 2pa5C 2qepC 3b7oC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36866.551 Da / Num. of mol.: 1 / Fragment: Tyrosine-protein phosphatase / Mutation: C1239S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRJ / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q12913, protein-tyrosine-phosphatase | ||||||
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#2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.01M NiCl2, 0.1M TRIS, pH 8.5, 1M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.98 Å / Num. obs: 15274 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.089 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.387 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2CFV Resolution: 2.3→46.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 11.948 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.442 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→46.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -7.3409 Å / Origin y: 29.388 Å / Origin z: -13.9498 Å
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