[English] 日本語
Yorodumi- PDB-4b04: Crystal structure of the Catalytic Domain of Human DUSP26 (C152S) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b04 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Catalytic Domain of Human DUSP26 (C152S) | ||||||
Components | DUAL SPECIFICITY PROTEIN PHOSPHATASE 26 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of MAPK cascade / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / positive regulation of cell adhesion / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of MAPK cascade / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / positive regulation of cell adhesion / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / p53 binding / negative regulation of ERK1 and ERK2 cascade / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.205 Å | ||||||
Authors | Won, E.-Y. / Lee, D.Y. / Park, S.G. / Yokoyama, S. / Kim, S.J. / Chi, S.-W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: High-Resolution Crystal Structure of the Catalytic Domain of Human Dual-Specificity Phosphatase 26 Authors: Won, E.-Y. / Xie, Y. / Takemoto, C. / Chen, L. / Liu, Z.-J. / Wang, B.C. / Lee, D. / Woo, E.-J. / Park, S.G. / Shirouzu, M. / Yokoyama, S. / Kim, S.J. / Chi, S.-W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4b04.cif.gz | 231 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4b04.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 4b04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b04_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4b04_full_validation.pdf.gz | 470.5 KB | Display | |
Data in XML | 4b04_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 4b04_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/4b04 ftp://data.pdbj.org/pub/pdb/validation_reports/b0/4b04 | HTTPS FTP |
-Related structure data
Related structure data | 2e0tSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18237.900 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 61-211 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL References: UniProt: Q9BV47, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 152 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 152 TO SER ...ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 43 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 31803 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 8.4 % / Biso Wilson estimate: 27.93 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.1 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E0T Resolution: 2.205→40.115 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 27.32 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.095 Å2 / ksol: 0.422 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.1 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.205→40.115 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|