+Open data
-Basic information
Entry | Database: PDB / ID: 2fh7 | ||||||
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Title | Crystal structure of the phosphatase domains of human PTP SIGMA | ||||||
Components | Receptor-type tyrosine-protein phosphatase S | ||||||
Keywords | HYDROLASE / receptor protein tyrosine phosphatase / Dual domain phosphatase / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / Receptor-type tyrosine-protein phosphatases / chondroitin sulfate binding / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development ...negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / Receptor-type tyrosine-protein phosphatases / 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 / Synaptic adhesion-like molecules / corpus callosum development / heparan sulfate proteoglycan binding / negative regulation of interferon-beta production / spinal cord development / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / ECM proteoglycans / cerebellum development / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampus development / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / cerebral cortex development / negative regulation of neuron projection development / presynaptic membrane / heparin binding / growth cone / perikaryon / axon / glutamatergic synapse / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Alvarado, J. / Udupi, R. / Smith, D. / Koss, J. / Wasserman, S.R. / Ozyurt, S. / Atwell, S. / Powell, A. / Kearins, M.C. / Rooney, I. ...Alvarado, J. / Udupi, R. / Smith, D. / Koss, J. / Wasserman, S.R. / Ozyurt, S. / Atwell, S. / Powell, A. / Kearins, M.C. / Rooney, I. / Maletic, M. / Bain, K.T. / Freeman, J.C. / Russell, M. / Thompson, D.A. / 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 | 2fh7.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fh7.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/2fh7 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/2fh7 | HTTPS FTP |
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-Related structure data
Related structure data | 1rxdC 2g59C 2hcmC 2hhlC 2hxpC 2hy3C 2i0oC 2i1yC 2i44C 2iq1C 2irmC 2isnC 2nv5C 2oycC 2p27C 2p4uC 2p69C 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC 1larS 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: 68703.688 Da / Num. of mol.: 1 / Fragment: Cytoplasmic phosphatase domains / Mutation: Residues 1365-1948 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ RIL / References: UniProt: Q13332, protein-tyrosine-phosphatase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein(10mg/ml) was crystallized in (15% PEG3350,100mM Succinic Acid)., pH 7.0, 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 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→25.76 Å / Num. obs: 55608 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.81→1.91 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 0.6 / Num. unique all: 7637 / Rsym value: 0.0115 / % possible all: 93.3 |
-Phasing
Phasing MR | Rfactor: 0.437 / Cor.coef. Fo:Fc: 0.52
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LAR Resolution: 2→24.67 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.802 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.172 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.698 Å2
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Refinement step | Cycle: LAST / Resolution: 2→24.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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