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Yorodumi- PDB-2g59: Crystal Structure of the Catalytic Domain of Protein Tyrosine Pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g59 | ||||||
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Title | Crystal Structure of the Catalytic Domain of Protein Tyrosine Phosphatase from Homo sapiens | ||||||
Components | Receptor-type tyrosine-protein phosphatase O | ||||||
Keywords | HYDROLASE / Protein Tyrosine Phosphatase / Dephosphorylation / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
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 / phosphatase activity / monocyte chemotaxis / 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 / lamellipodium / negative regulation of neuron projection development / 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: 2.19 Å | ||||||
Authors | Kumaran, D. / Swaminathan, S. / Burley, S.K. / 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 | 2g59.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g59.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 2g59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/2g59 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/2g59 | HTTPS FTP |
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-Related structure data
Related structure data | 1rxdC 2fh7C 2hcmC 2hhlC 2hxpC 2hy3C 2i0oC 2i1yC 2i44C 2iq1C 2irmC 2isnC 2nv5C 2oycC 2p27C 2p4uC 2p69C 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC 2ahsS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 34942.656 Da / Num. of mol.: 2 / Fragment: Protein tyrosine phosphatase, catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRO, GLEPP1, PTPU2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16827, protein-tyrosine-phosphatase #2: Chemical | #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: 2.37 Å3/Da / Density % sol: 48.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-Tris, 2.0 M Sodium Chloride, 5% PEG 3350, 5 mM Calcium Chloride, 10 mM Sodium Phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. all: 33737 / Num. obs: 33737 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.098 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 2.5 % / Num. unique all: 3127 / Rsym value: 0.252 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2AHS Resolution: 2.19→31.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 152543.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The residues listed in remark 465 were not modeled due to lack of electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.9285 Å2 / ksol: 0.366282 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→31.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.33 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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