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Yorodumi- PDB-2nv5: Crystal structure of a C-terminal phosphatase domain of Rattus no... -
+Open data
-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) | ||||||
Components | PTPRD, PHOSPHATASE | ||||||
Keywords | HYDROLASE / PHOSPHATASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information 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 / synaptic membrane adhesion / regulation of postsynaptic density assembly / 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 / cerebellum development / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampus development / synapse organization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / cerebral cortex development / negative regulation of neuron projection development / heparin binding / growth cone / perikaryon / axon / glutamatergic synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nv5.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nv5.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/2nv5 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/2nv5 | HTTPS FTP |
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-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 (ref.) |
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Similar structure data | |
Other databases |
-Links
-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.) Rattus norvegicus (Norway rat) / Gene: PTPRD / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 10947503, UniProt: Q64605*PLUS #2: 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: 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: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.853 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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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