+Open data
-Basic information
Entry | Database: PDB / ID: 6ntp | ||||||||||||
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Title | PTP1B Domain of PTP1B-LOV2 Chimera | ||||||||||||
Components | Tyrosine-protein phosphatase non-receptor type 1,NPH1-1 | ||||||||||||
Keywords | HYDROLASE / Protein tyrosine phosphatase / protein phosphorylation / signaling / diabetes / obesity / cancer | ||||||||||||
Function / homology | Function and homology information blue light photoreceptor activity / 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 ...blue light photoreceptor activity / 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 / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / 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 / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / 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 / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / 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 / non-specific serine/threonine protein kinase / mitochondrial matrix / cadherin binding / phosphorylation / protein serine/threonine kinase activity / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Avena sativa (oats) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||||||||
Authors | Hongdusit, A. / Sankaran, B. / Zwart, P.H. / Fox, J.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2020 Title: Minimally disruptive optical control of protein tyrosine phosphatase 1B. Authors: Hongdusit, A. / Zwart, P.H. / Sankaran, B. / Fox, J.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ntp.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ntp.ent.gz | 107.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ntp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ntp_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 6ntp_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 6ntp_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6ntp_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/6ntp ftp://data.pdbj.org/pub/pdb/validation_reports/nt/6ntp | HTTPS FTP |
-Related structure data
Related structure data | 3a5jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52150.102 Da / Num. of mol.: 1 / Fragment: residues 2-282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Avena sativa (oats) Gene: PTPN1, PTP1B, NPH1-1 / Production host: Escherichia coli (E. coli) References: UniProt: P18031, UniProt: O49003, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-MG / |
#3: 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: 2.33 Å3/Da / Density % sol: 47.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, 200 mM magnesium acetate, and 14% polyethylene glycol 8000, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99994 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99994 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→52.87 Å / Num. obs: 39530 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rsym value: 0.025 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.89→1.92 Å / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 9.1 / Num. unique obs: 1936 / CC1/2: 1 / Rpim(I) all: 0.025 / Rrim(I) all: 0.075 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3a5j Resolution: 1.89→44.67 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.223 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.375 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→44.67 Å
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