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Yorodumi- PDB-4woh: Structure of of human dual-specificity phosphatase 22 (E24A/K28A/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4woh | ||||||
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Title | Structure of of human dual-specificity phosphatase 22 (E24A/K28A/K30A/C88S) complexed with 4-nitrophenolphosphate | ||||||
Components | Dual specificity protein phosphatase 22 | ||||||
Keywords | HYDROLASE / dual specificity phosphatase / JSP-1 / pNPP | ||||||
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 / Resolution: 1.34 Å | ||||||
Authors | Lountos, G.T. / Cherry, S. / Tropea, J.E. / Waugh, D.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate. Authors: Lountos, G.T. / Cherry, S. / Tropea, J.E. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4woh.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4woh.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 4woh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4woh_validation.pdf.gz | 456.3 KB | Display | wwPDB validaton report |
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Full document | 4woh_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 4woh_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 4woh_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/4woh ftp://data.pdbj.org/pub/pdb/validation_reports/wo/4woh | HTTPS FTP |
-Related structure data
Related structure data | 1wrmS 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
#1: Protein | Mass: 18548.002 Da / Num. of mol.: 1 / Mutation: E24A/K28A/K30A/C88S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP22, JSP1, LMWDSP2, MKPX / Plasmid: pJT294 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NRW4, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-4NP / |
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 21 mg/mL protein incubated with 10 mM 4-ntirophenolphosphate well solution: 0.1M Tris pH 8.5, 0.2M magnesium chloride, 20% w/v polyethylene glycol 3350 PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→50 Å / Num. obs: 37336 / % possible obs: 95.5 % / Redundancy: 3.7 % / Rsym value: 0.035 / Net I/σ(I): 48.2 |
Reflection shell | Resolution: 1.34→1.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 4.2 / % possible all: 78.8 |
-Processing
Software | Name: REFMAC / Version: 5.5.0104 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1wrm Resolution: 1.34→44.77 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.363 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.159 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→44.77 Å
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