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Open data
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Basic information
Entry | Database: PDB / ID: 4jmj | ||||||
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Title | Structure of dusp11 | ||||||
![]() | RNA/RNP complex-1-interacting phosphatase | ||||||
![]() | HYDROLASE / alpha/beta hydrolase | ||||||
Function / homology | ![]() protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / intercellular bridge / phosphatase activity / RNA processing / protein dephosphorylation / protein tyrosine phosphatase activity / fibrillar center / nuclear speck ...protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / intercellular bridge / phosphatase activity / RNA processing / protein dephosphorylation / protein tyrosine phosphatase activity / fibrillar center / nuclear speck / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeong, D.G. / Kim, S.J. / Ryu, S.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.9 KB | Display | ![]() |
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PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
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Full document | ![]() | 440.8 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jmkC ![]() 4jnbC ![]() 4ki9C ![]() 1yn9S C: citing same article ( S: Starting model for refinement |
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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: 21309.303 Da / Num. of mol.: 1 / Fragment: UNP residues 28-208 / Mutation: C125S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75319, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2006 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→40 Å / Num. all: 9356 / Num. obs: 9276 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.38→2.47 Å / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YN9 Resolution: 2.382→27.36 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 1.32 / Phase error: 26.28 / 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 | Biso max: 138.94 Å2 / Biso mean: 61.4401 Å2 / Biso min: 25.35 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.382→27.36 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: 35.9787 Å / Origin y: 11.8223 Å / Origin z: 3.0491 Å
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Refinement TLS group | Selection details: all |