+Open data
-Basic information
Entry | Database: PDB / ID: 2gjt | ||||||
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Title | Crystal structure of the human receptor phosphatase PTPRO | ||||||
Components | Receptor-type tyrosine-protein phosphatase PTPRO | ||||||
Keywords | HYDROLASE / Tyrosine phosphatase / PTPRO / GLEPP1 / PTPU2 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information slit diaphragm assembly / negative regulation of retinal ganglion cell axon guidance / regulation of glomerular filtration / negative regulation of glomerular filtration / Signaling by NTRK3 (TRKC) / podocyte differentiation / transmembrane receptor protein tyrosine phosphatase activity / Wnt-protein binding / glomerulus development / negative regulation of cell-substrate adhesion ...slit diaphragm assembly / negative regulation of retinal ganglion cell axon guidance / regulation of glomerular filtration / negative regulation of glomerular filtration / Signaling by NTRK3 (TRKC) / podocyte differentiation / transmembrane receptor protein tyrosine phosphatase activity / Wnt-protein binding / glomerulus development / negative regulation of cell-substrate adhesion / lamellipodium assembly / regulation of synapse organization / monocyte chemotaxis / phosphatase activity / peptidyl-tyrosine dephosphorylation / lateral plasma membrane / GABA-ergic synapse / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / axon guidance / postsynaptic density membrane / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / negative regulation of neuron projection development / lamellipodium / growth cone / dendritic spine / neuron projection / cadherin binding / apical plasma membrane / axon / glutamatergic synapse / protein homodimerization activity / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Barr, A. / Ugochukwu, E. / Eswaran, J. / Das, S. / Niesen, F. / Savitsky, P. / Turnbull, A. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...Barr, A. / Ugochukwu, E. / Eswaran, J. / Das, S. / Niesen, F. / Savitsky, P. / Turnbull, A. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / von Delft, F. / Papagrigoriou, E. / 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 | 2gjt.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gjt.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/2gjt ftp://data.pdbj.org/pub/pdb/validation_reports/gj/2gjt | HTTPS FTP |
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-Related structure data
Related structure data | 2ahsSC 2b49C 2cfvC 2cjzC 2h4vC 2i75C 2jjdC 2nlkC 2nz6C 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
#1: Protein | Mass: 34634.383 Da / Num. of mol.: 2 / Fragment: residues 916-1208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRO, GLEPP1, PTPU2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q16827, protein-tyrosine-phosphatase #2: Chemical | ChemComp-CL / #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: 2.77 Å3/Da / Density % sol: 55.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Isopropanol, PEG4K, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→42.91 Å / Num. all: 41322 / Num. obs: 41322 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.15→2.25 Å / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AHS Resolution: 2.15→42.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.179 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.179 / 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: 29.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→42.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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