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Open data
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Basic information
Entry | Database: PDB / ID: 6j6u | ||||||
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Title | Rat PTPRZ D1-D2 domain | ||||||
![]() | Receptor-type tyrosine-protein phosphatase zeta | ||||||
![]() | HYDROLASE / Protein Tyrosine Phosphatase | ||||||
Function / homology | ![]() perineuronal net / : / regulation of oligodendrocyte progenitor proliferation / : / : / Other interleukin signaling / negative regulation of dendrite development / positive regulation of Schwann cell migration / positive regulation of neuron migration / axonal fasciculation ...perineuronal net / : / regulation of oligodendrocyte progenitor proliferation / : / : / Other interleukin signaling / negative regulation of dendrite development / positive regulation of Schwann cell migration / positive regulation of neuron migration / axonal fasciculation / positive regulation of dendrite development / negative regulation of cell-substrate adhesion / regulation of myelination / positive regulation of oligodendrocyte differentiation / regulation of dendrite morphogenesis / fibroblast growth factor binding / oligodendrocyte differentiation / phosphatase activity / peptidyl-tyrosine dephosphorylation / neuron development / hematopoietic progenitor cell differentiation / protein dephosphorylation / protein-tyrosine-phosphatase / axonogenesis / extracellular matrix / filopodium / protein tyrosine phosphatase activity / hippocampus development / visual learning / brain development / ruffle membrane / positive regulation of neuron projection development / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / integrin binding / lamellipodium / growth cone / postsynaptic membrane / negative regulation of neuron apoptotic process / dendritic spine / learning or memory / positive regulation of cell migration / negative regulation of cell population proliferation / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / extracellular space / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sugawara, H. | ||||||
![]() | ![]() Title: A head-to-toe dimerization has physiological relevance for ligand-induced inactivation of protein tyrosine receptor type Z. Authors: Fujikawa, A. / Sugawara, H. / Tanga, N. / Ishii, K. / Kuboyama, K. / Uchiyama, S. / Suzuki, R. / Noda, M. #1: ![]() Title: Small-molecule inhibition of PTPRZ suppresses tumor growth in a rat model of glioblastoma. Authors: Fujikawa, A. / Nagahira, A. / Sugawara, H. / Ishii, K. / Imajo, S. / Matsumoto, M. / Kuboyama, K. / Suzuki, R. / Tanga, N. / Noda, M. / Uchiyama, S. / Tomoo, T. / Ogata, A. / Masumura, M. / Noda, M. #2: ![]() Title: Targeting PTPRZ inhibits stem cell-like properties and tumorigenicity in glioblastoma cells. Authors: Fujikawa, A. / Sugawara, H. / Tanaka, T. / Matsumoto, M. / Kuboyama, K. / Suzuki, R. / Tanga, N. / Ogata, A. / Masumura, M. / Noda, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224 KB | Display | ![]() |
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PDB format | ![]() | 177 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
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Full document | ![]() | 461.1 KB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nlkS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1699 - 2285 / Label seq-ID: 1 - 587
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Components
#1: Protein | Mass: 70564.500 Da / Num. of mol.: 2 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: 2.19 Å3/Da / Density % sol: 43.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14% PEG3350, 0.15M potassium fluoride, bis-Tris propane pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.32→100 Å / Num. obs: 15767 / % possible obs: 84 % / Redundancy: 3.3 % / Net I/σ(I): 13 |
Reflection shell | Resolution: 3.32→3.41 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NLK Resolution: 3.32→38.97 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.823 / SU B: 29.021 / SU ML: 0.49 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.573 Å2
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Refinement step | Cycle: 1 / Resolution: 3.32→38.97 Å
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Refine LS restraints |
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