+Open data
-Basic information
Entry | Database: PDB / ID: 2i1y | ||||||
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Title | Crystal structure of the phosphatase domain of human PTP IA-2 | ||||||
Components | Receptor-type tyrosine-protein phosphatase | ||||||
Keywords | HYDROLASE / Receptor-type protein tyrosine phosphatase precursor / phosphatase / structural genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information dense core granule maturation / positive regulation of type B pancreatic cell proliferation / regulation of secretion / luteinization / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / transport vesicle membrane / spectrin binding / ubiquitin-like protein ligase binding / transcription factor binding ...dense core granule maturation / positive regulation of type B pancreatic cell proliferation / regulation of secretion / luteinization / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / transport vesicle membrane / spectrin binding / ubiquitin-like protein ligase binding / transcription factor binding / axon terminus / secretory granule / response to reactive oxygen species / perikaryon / endosome / neuronal cell body / synapse / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Faber-Barata, J. / Patskovsky, Y. / Alvarado, J. / Smith, D. / Koss, J. / Wasserman, S.R. / Ozyurt, S. / Atwell, S. / Powell, A. / Kearins, M.C. ...Faber-Barata, J. / Patskovsky, Y. / Alvarado, J. / Smith, D. / Koss, J. / Wasserman, S.R. / Ozyurt, S. / Atwell, S. / Powell, A. / Kearins, M.C. / Maletic, M. / Rooney, I. / Bain, K.T. / Freeman, M. / Russell, J.C. / Thompson, D.A. / 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 | 2i1y.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i1y.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 2i1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/2i1y ftp://data.pdbj.org/pub/pdb/validation_reports/i1/2i1y | HTTPS FTP |
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-Related structure data
Related structure data | 1rxdC 2fh7SC 2g59C 2hcmC 2hhlC 2hxpC 2hy3C 2i0oC 2i44C 2iq1C 2irmC 2isnC 2nv5C 2oycC 2p27C 2p4uC 2p69C 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 34293.023 Da / Num. of mol.: 2 / Fragment: Tyrosine-protein phosphatase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRN, ICA3, ICA512 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CODON+ RIL / References: UniProt: Q16849, 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: 2.23 Å3/Da / Density % sol: 48.56 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25% PEG3350, 100 MM BIS-TRIS, 200 MM AMMONIUM ACETATE, PH 6.0, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 / Wavelength: 0.93971 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 7, 2006 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.23→50 Å / Num. all: 32726 / Num. obs: 32726 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.225 / Rsym value: 0.191 / Net I/σ(I): 2.7 | |||||||||
Reflection shell | Resolution: 2.23→2.34 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.5 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FH7 Resolution: 2.23→19.73 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.039 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.077 Å2
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Refinement step | Cycle: LAST / Resolution: 2.23→19.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.23→2.288 Å / Total num. of bins used: 20
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