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Yorodumi- PDB-6b90: Multiconformer model of apo WT PTP1B with glycerol at 100 K (ALTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b90 | ||||||
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Title | Multiconformer model of apo WT PTP1B with glycerol at 100 K (ALTERNATIVE REFINEMENT OF PDB 1SUG showing conformational heterogeneity) | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 1 | ||||||
Keywords | SIGNALING PROTEIN / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multitemperature / multiconformer | ||||||
Function / homology | Function and homology information regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / positive regulation of protein tyrosine kinase activity / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / Growth hormone receptor signaling / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / negative regulation of MAP kinase activity / protein-tyrosine-phosphatase / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å | ||||||
Authors | Keedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / von Delft, F. / Wells, J.A. / Fraser, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2004 Title: Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B. Authors: Pedersen, A.K. / Peters G, G.u. / Moller, K.B. / Iversen, L.F. / Kastrup, J.S. | ||||||
History |
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Remark 0 | THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 1SUG DETERMINED BY A. ...THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 1SUG DETERMINED BY A.K.PEDERSEN,G.G.H.PETERS,K.B.MOLLER,L.F.IVERSEN,J.S.KASTRUP |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b90.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b90.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 6b90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/6b90 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/6b90 | HTTPS FTP |
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-Related structure data
Related structure data | 5qdeC 5qdfC 5qdgC 5qdhC 5qdiC 5qdjC 5qdkC 5qdlC 5qdmC 5qdnC 5qdoC 5qdpC 5qdqC 5qdrC 5qdsC 5qdtC 5qduC 5qdvC 5qdwC 5qdxC 5qdyC 5qdzC 5qe0C 5qe1C 5qe2C 5qe3C 5qe4C 5qe5C 5qe6C 5qe7C 5qe8C 5qe9C 5qeaC 5qebC 5qecC 5qedC 5qeeC 5qefC 5qegC 5qehC 5qeiC 5qejC 5qekC 5qelC 5qemC 5qenC 5qeoC 5qepC 5qeqC 5qerC 5qesC 5qetC 5qeuC 5qevC 5qewC 5qexC 5qeyC 5qezC 5qf0C 5qf1C 5qf2C 5qf3C 5qf4C 5qf5C 5qf6C 5qf7C 5qf8C 5qf9C 5qfaC 5qfbC 5qfcC 5qfdC 5qfeC 5qffC 5qfgC 5qfhC 5qfiC 5qfjC 5qfkC 5qflC 5qfmC 5qfnC 5qfoC 5qfpC 5qfqC 5qfrC 5qfsC 5qftC 5qfuC 5qfvC 5qfwC 5qfxC 5qfyC 5qfzC 5qg0C 5qg1C 5qg2C 5qg3C 5qg4C 5qg5C 5qg6C 5qg7C 5qg8C 5qg9C 5qgaC 5qgbC 5qgcC 5qgdC 5qgeC 5qgfC 6b8eC 6b8tC 6b8xC 6b8zC 6b95C 6baiC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37365.637 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase | ||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-TRS / | #4: 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: 3.36 Å3/Da / Density % sol: 63.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: well solution: PEG 8000, magnesium acetate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 28, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45 Å / Num. obs: 34528 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.14 Å2 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3375 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.95→35.817 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.33 Details: Re-refinement of 1sug using multiconformer modeling with qFit and manual editing, then refinement with PHENIX
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.89 Å2 / Biso mean: 32.3237 Å2 / Biso min: 11.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→35.817 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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