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Yorodumi- PDB-4y2e: Crystal structure of the catalytic domain of human dual-specifici... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y2e | ||||||
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Title | Crystal structure of the catalytic domain of human dual-specificity phosphatase 7 (C232S) | ||||||
Components | Dual specificity protein phosphatase 7 | ||||||
Keywords | HYDROLASE / dual specificity phosphatase | ||||||
Function / homology | Function and homology information : / : / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / peptidyl-threonine dephosphorylation / protein tyrosine/serine/threonine phosphatase activity / RAF-independent MAPK1/3 activation / ERKs are inactivated / mitogen-activated protein kinase binding / protein-serine/threonine phosphatase ...: / : / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / peptidyl-threonine dephosphorylation / protein tyrosine/serine/threonine phosphatase activity / RAF-independent MAPK1/3 activation / ERKs are inactivated / mitogen-activated protein kinase binding / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein tyrosine phosphatase activity / Negative regulation of MAPK pathway / MAPK cascade / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Lountos, G.T. / Austin, B.P. / Tropea, J.E. / Waugh, D.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Structure of human dual-specificity phosphatase 7, a potential cancer drug target. Authors: Lountos, G.T. / Austin, B.P. / 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 | 4y2e.cif.gz | 145.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y2e.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 4y2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/4y2e ftp://data.pdbj.org/pub/pdb/validation_reports/y2/4y2e | HTTPS FTP |
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-Related structure data
Related structure data | 3lj8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16761.184 Da / Num. of mol.: 4 / Fragment: catalytic domain (UNP residues 240-388) / Mutation: C232S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP7, PYST2 / Plasmid: pBA2529 / Production host: Escherichia coli (E. coli) References: UniProt: Q16829, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase #2: Chemical | ChemComp-PO4 / #3: 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: 2.3 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes,MOPS pH 7.5, 0.009 nitrate-sulfate-phosphate mixture, 37.5% v/v MPD-PEG1000-PEG3350; Morpheus Crystallization screen #32 PH range: 7.5 |
-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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. obs: 70511 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LJ8 Resolution: 1.67→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.844 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / 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: 9.848 Å2
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Refinement step | Cycle: 1 / Resolution: 1.67→50 Å
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Refine LS restraints |
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