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Yorodumi- PDB-2hy3: Crystal structure of the human tyrosine receptor phosphate gamma ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hy3 | ||||||
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Title | Crystal structure of the human tyrosine receptor phosphate gamma in complex with vanadate | ||||||
Components | Receptor-type tyrosine-protein phosphatase gamma | ||||||
Keywords | HYDROLASE / twisted mixed beta-sheets flanked by {alpha}-helices / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of neuron projection development / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Jin, X. / Min, T. / Bera, A. / Mu, H. / Sauder, J.M. / Freeman, J.C. / Reyes, C. / Smith, D. / Wasserman, S.R. / Burley, S.K. ...Jin, X. / Min, T. / Bera, A. / Mu, H. / Sauder, J.M. / Freeman, J.C. / Reyes, C. / Smith, D. / Wasserman, S.R. / Burley, S.K. / Shapiro, L. / 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 | 2hy3.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hy3.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 2hy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/2hy3 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/2hy3 | HTTPS FTP |
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-Related structure data
Related structure data | 1rxdC 2fh7C 2g59C 2hcmC 2hhlC 2hxpC 2i0oC 2i1yC 2i44C 2iq1C 2irmC 2isnC 2nv5C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 826 - 1122 / Label seq-ID: 9 - 305
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-Components
#1: Protein | Mass: 36417.207 Da / Num. of mol.: 2 / Fragment: residues 819-1130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRG / Plasmid: pSGX4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23470, 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12% PEG3350, 0.1M Tris, 0.3M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97891 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 24687 / Num. obs: 20061 / % possible obs: 87 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→17 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.882 / SU B: 25.526 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Used weighted full matrix least squares procedure.
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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: 40.551 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2217 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.666 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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