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Yorodumi- PDB-4ki9: Crystal structure of the catalytic domain of human DUSP12 at 2.0 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ki9 | ||||||
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Title | Crystal structure of the catalytic domain of human DUSP12 at 2.0 A resolution | ||||||
Components | Dual specificity protein phosphatase 12 | ||||||
Keywords | HYDROLASE / Dual specificity phosphatase / Protein tyrosine phosphatase / Dusp / PTP | ||||||
Function / homology | Function and homology information protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein modification process / kinase binding / zinc ion binding ...protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein modification process / kinase binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Jeon, T.J. / Chien, P.N. / Ku, B. / Kim, S.J. / Ryu, S.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: The family-wide structure and function of human dual-specificity protein phosphatases Authors: Jeong, D.G. / Wei, C.H. / Ku, B. / Jeon, T.J. / Chien, P.N. / Kim, J.K. / Park, S.Y. / Hwang, H.S. / Ryu, S.Y. / Park, H. / Kim, D.S. / Kim, S.J. / Ryu, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ki9.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ki9.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ki9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/4ki9 ftp://data.pdbj.org/pub/pdb/validation_reports/ki/4ki9 | HTTPS FTP |
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-Related 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: 18100.650 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP RESIDUES 27-189 / Mutation: C97A, C115S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP12 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UNI6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Method: vapor diffusion Details: 16% PEG 8000, 38% monopotassium phosphate, 20% glycerol, VAPOR DIFFUSION |
-Data collection
Diffraction |
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Diffraction source |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→32.7 Å / Num. all: 11586 / Num. obs: 11473 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.698 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 19.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→32.698 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -4.483 Å / Origin y: 1.6256 Å / Origin z: -17.4101 Å
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Refinement TLS group | Selection details: ALL |