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- PDB-4qun: Crystal structure of the PTPN3 (PTPH1) catalytic domain C842S mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qun | ||||||
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Title | Crystal structure of the PTPN3 (PTPH1) catalytic domain C842S mutant | ||||||
![]() | Tyrosine-protein phosphatase non-receptor type 3 | ||||||
![]() | HYDROLASE / Alpha Beta | ||||||
Function / homology | ![]() regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transporter activity / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase ...regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transporter activity / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / liver regeneration / EGFR downregulation / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / MAPK cascade / ATPase binding / cytoskeleton / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chen, K.E. / Meng, T.C. / Wang, A.H.J. | ||||||
![]() | ![]() Title: Reciprocal allosteric regulation of p38 gamma and PTPN3 involves a PDZ domain-modulated complex formation. Authors: Chen, K.E. / Lin, S.Y. / Wu, M.J. / Ho, M.R. / Santhanam, A. / Chou, C.C. / Meng, T.C. / Wang, A.H.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.1 KB | Display | ![]() |
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PDB format | ![]() | 103.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.1 KB | Display | ![]() |
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Full document | ![]() | 463.4 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qumC ![]() 2b49S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34931.672 Da / Num. of mol.: 2 / Fragment: Catalytic domain (UNP RESIDUES 628-909) / Mutation: C842S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes, 12% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 9, 2012 |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. all: 53391 / Num. obs: 53391 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5319 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 2B49 Resolution: 1.86→45.764 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.92 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→45.764 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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