+Open data
-Basic information
Entry | Database: PDB / ID: 6lot | ||||||
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Title | Crystal structure of DUSP22 mutant_N128D | ||||||
Components | Dual specificity protein phosphatase 22 | ||||||
Keywords | HYDROLASE / DUSP22 / atypical DUSPs / Cysteine based protein tyrosine phosphatases (Cys-based PTPs) / active site of DUSPs | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å | ||||||
Authors | Lai, C.H. / Lyu, P.C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Int J Mol Sci / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lot.cif.gz | 47.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lot.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 6lot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lot_validation.pdf.gz | 810.6 KB | Display | wwPDB validaton report |
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Full document | 6lot_full_validation.pdf.gz | 811.6 KB | Display | |
Data in XML | 6lot_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 6lot_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/6lot ftp://data.pdbj.org/pub/pdb/validation_reports/lo/6lot | HTTPS FTP |
-Related structure data
Related structure data | 6l1sC 6lmyC 6louC 6lvqC 7c8sC 1wrmS 6kmi C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17812.367 Da / Num. of mol.: 1 / Mutation: N128D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP22, JSP1, LMWDSP2, MKPX / Production host: Escherichia coli (E. coli) References: UniProt: Q9NRW4, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 0.1 M PIPES, 30% PEG 3,350, 0.2 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→30 Å / Num. obs: 20649 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Χ2: 1.007 / Net I/σ(I): 16.6 / Num. measured all: 72939 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1WRM Resolution: 1.69→25.8736 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.22 Å2 / Biso mean: 25.5385 Å2 / Biso min: 9.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.69→25.8736 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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