+Open data
-Basic information
Entry | Database: PDB / ID: 5y16 | ||||||||||||
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Title | Crystal structure of human DUSP28(Y102H) | ||||||||||||
Components | Dual specificity phosphatase 28 | ||||||||||||
Keywords | HYDROLASE / DUSP28 / dual-specificity phosphatase / DUSP / protein tyrosine phosphatase / PTP | ||||||||||||
Function / homology | Function and homology information protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å | ||||||||||||
Authors | Ku, B. / Kim, M. / Kim, S.J. / Ryu, S.E. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: PLoS ONE / Year: 2017 Title: Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28 Authors: Ku, B. / Hong, W. / Keum, C.W. / Kim, M. / Ryu, H. / Jeon, D. / Shin, H.C. / Kim, J.H. / 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 | 5y16.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y16.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 5y16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/5y16 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/5y16 | HTTPS FTP |
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-Related structure data
Related structure data | 5y15SC S: Starting model for refinement C: citing same article (ref.) |
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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: 20576.473 Da / Num. of mol.: 2 / Mutation: R59Q, Y102H, C103S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP28 / Production host: Escherichia coli (E. coli) References: UniProt: Q4G0W2, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris-HCl pH 8.5, 100 mM NaCl, 28% [w/v] polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 12461 / % possible obs: 93.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.309 / Rsym value: 0.309 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y15 Resolution: 2.399→27.634 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 23.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.399→27.634 Å
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Refine LS restraints |
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LS refinement shell |
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