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Open data
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Basic information
Entry | Database: PDB / ID: 6l1s | ||||||
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Title | Crystal structure of DUSP22 mutant_C88S | ||||||
![]() | Dual specificity protein phosphatase 22 | ||||||
![]() | HYDROLASE / DUSP22 / atypical DUSPs / Cysteine based protein tyrosine phosphatases (Cys-based PTPs) / active site of DUSPs | ||||||
Function / homology | ![]() negative regulation of non-membrane spanning protein tyrosine kinase activity / negative regulation of T cell mediated immunity / leading edge of lamellipodium / negative regulation of T cell activation / protein tyrosine/serine/threonine phosphatase activity / negative regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / myosin phosphatase activity / protein-serine/threonine phosphatase / filamentous actin ...negative regulation of non-membrane spanning protein tyrosine kinase activity / negative regulation of T cell mediated immunity / leading edge of lamellipodium / negative regulation of T cell activation / protein tyrosine/serine/threonine phosphatase activity / negative regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / myosin phosphatase activity / protein-serine/threonine phosphatase / filamentous actin / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / dephosphorylation / cellular response to epidermal growth factor stimulus / negative regulation of cell migration / protein-tyrosine-phosphatase / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / protein tyrosine phosphatase activity / positive regulation of JNK cascade / regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / signal transduction / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lai, C.H. / Chang, C.C. / Lyu, P.C. | ||||||
![]() | ![]() Title: Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases. Authors: Lai, C.H. / Chang, C.C. / Chuang, H.C. / Tan, T.H. / Lyu, P.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.9 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 754.1 KB | Display | ![]() |
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Full document | ![]() | 754 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lmyC ![]() 6lotC ![]() 6louC ![]() 6lvqC ![]() 7c8sC ![]() 1wrmS ![]() 6kmi 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 17795.314 Da / Num. of mol.: 1 / Mutation: C88S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NRW4, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 0.2M Imidazole, 0.4M NaH2PO4/1.6M K2HPO4, 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 10, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.36→30 Å / Num. obs: 36409 / % possible obs: 97.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.02 / Rrim(I) all: 0.039 / Χ2: 1.046 / Net I/σ(I): 20.6 / Num. measured all: 137519 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WRM Resolution: 1.3611→22.3308 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.17 Å2 / Biso mean: 19.1077 Å2 / Biso min: 8.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3611→22.3308 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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