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- PDB-2nv5: Crystal structure of a C-terminal phosphatase domain of Rattus no... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nv5 | ||||||
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Title | Crystal structure of a C-terminal phosphatase domain of Rattus norvegicus ortholog of human protein tyrosine phosphatase, receptor type, D (PTPRD) | ||||||
![]() | PTPRD, PHOSPHATASE | ||||||
![]() | HYDROLASE / PHOSPHATASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() Receptor-type tyrosine-protein phosphatases / negative regulation of toll-like receptor 9 signaling pathway / : / : / negative regulation of interferon-alpha production / : / chondroitin sulfate binding / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier ...Receptor-type tyrosine-protein phosphatases / negative regulation of toll-like receptor 9 signaling pathway / : / : / negative regulation of interferon-alpha production / : / chondroitin sulfate binding / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of axon extension / corpus callosum development / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / Synaptic adhesion-like molecules / spinal cord development / phosphoprotein phosphatase activity / regulation of presynapse assembly / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / cerebellum development / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampus development / synapse organization / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cerebral cortex development / negative regulation of neuron projection development / heparin binding / growth cone / perikaryon / axon / glutamatergic synapse / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bonanno, J.B. / Gilmore, J. / Bain, K.T. / Iizuka, M. / Xu, W. / Wasserman, S. / Smith, D. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Structural genomics of protein phosphatases. Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.6 KB | Display | ![]() |
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PDB format | ![]() | 153.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.6 KB | Display | ![]() |
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Full document | ![]() | 451 KB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 55.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rxdC ![]() 2fh7C ![]() 2g59C ![]() 2hcmC ![]() 2hhlC ![]() 2hxpC ![]() 2hy3C ![]() 2i0oC ![]() 2i1yC ![]() 2i44C ![]() 2iq1C ![]() 2irmC ![]() 2isnC ![]() 2oycC ![]() 2p27C ![]() 2p4uC ![]() 2p69C ![]() 2p8eC ![]() 2pbnC ![]() 2q5eC ![]() 2qjcC ![]() 2r0bC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34345.742 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 30% PEG MME 2K, 100mM potassium thiocyanate, pH 7.0, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 2, 2006 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.89 Å / Num. all: 85072 / Num. obs: 83626 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 3.4 / Num. measured all: 149687 / Num. unique all: 11897 / Rsym value: 0.837 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.197 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.053 Å / Total num. of bins used: 20
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