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Yorodumi- PDB-6xed: Crystal Structure of the PTP1B YopH WPD loop Chimera 3 bound to t... -
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-Basic information
Entry | Database: PDB / ID: 6xed | ||||||
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Title | Crystal Structure of the PTP1B YopH WPD loop Chimera 3 bound to tungstate | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 1 | ||||||
Keywords | HYDROLASE / PTP1B / tyrosine phosphatase / WPD loop | ||||||
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 / 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 / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / 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 / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.795 Å | ||||||
Authors | Olsen, K.J. / Shen, R. / Johnson, S.J. / Hengge, A.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem Sci / Year: 2022 Title: Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases. Authors: Shen, R. / Crean, R.M. / Olsen, K.J. / Corbella, M. / Calixto, A.R. / Richan, T. / Brandao, T.A.S. / Berry, R.D. / Tolman, A. / Loria, J.P. / Johnson, S.J. / Kamerlin, S.C.L. / Hengge, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xed.cif.gz | 150.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xed.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 6xed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xed_validation.pdf.gz | 467.1 KB | Display | wwPDB validaton report |
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Full document | 6xed_full_validation.pdf.gz | 467 KB | Display | |
Data in XML | 6xed_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 6xed_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/6xed ftp://data.pdbj.org/pub/pdb/validation_reports/xe/6xed | HTTPS FTP |
-Related structure data
Related structure data | 6xe8C 6xeaC 6xeeC 6xefC 6xegC 7s4fC 3qkpS S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37331.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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-Non-polymers , 5 types, 298 molecules
#2: Chemical | ChemComp-WO4 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 3.29 Å3/Da / Density % sol: 61.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: tris hydrochloride pH 7.8, magnesium acetate tetrahydrate, PEG 8000 and benzamidine PH range: 7.8-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.795→50 Å / Num. obs: 44952 / % possible obs: 100 % / Redundancy: 16.4 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.026 / Rrim(I) all: 0.112 / Χ2: 1.037 / Net I/σ(I): 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QKP Resolution: 1.795→44.435 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.23 Å2 / Biso mean: 32.6017 Å2 / Biso min: 17.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.795→44.435 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -44.474 Å / Origin y: 17.0629 Å / Origin z: 15.1562 Å
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Refinement TLS group |
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