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Yorodumi- PDB-1ym9: Crystal structure of the CDC25B phosphatase catalytic domain with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ym9 | ||||||
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Title | Crystal structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfinic form | ||||||
Components | M-phase inducer phosphatase 2 | ||||||
Keywords | HYDROLASE / CELL CYCLE / Sulfinic Cysteine | ||||||
Function / homology | Function and homology information positive regulation of G2/MI transition of meiotic cell cycle / female meiosis I / oocyte maturation / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of cytokinesis / phosphoprotein phosphatase activity / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of mitotic cell cycle ...positive regulation of G2/MI transition of meiotic cell cycle / female meiosis I / oocyte maturation / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of cytokinesis / phosphoprotein phosphatase activity / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of mitotic cell cycle / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / spindle pole / G2/M transition of mitotic cell cycle / mitotic cell cycle / cell division / protein phosphorylation / centrosome / positive regulation of cell population proliferation / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Buhrman, G.K. / Parker, B. / Sohn, J. / Rudolph, J. / Mattos, C. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural Mechanism of Oxidative Regulation of the Phosphatase Cdc25B via an Intramolecular Disulfide Bond Authors: Buhrman, G.K. / Parker, B. / Sohn, J. / Rudolph, J. / Mattos, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ym9.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ym9.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 1ym9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ym9_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 1ym9_full_validation.pdf.gz | 423.6 KB | Display | |
Data in XML | 1ym9_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1ym9_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1ym9 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1ym9 | HTTPS FTP |
-Related structure data
Related structure data | 1ymdC 1ymkC 1ymlC 1ys0C 1qb0S C: citing same article (ref.) S: Starting model for refinement |
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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: 20713.801 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC25B, CDC25HU2 / Production host: Escherichia coli (E. coli) / References: UniProt: P30305, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-CL / |
#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: 2.92 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.25 Details: DTT, Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | 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→35.44 Å / Num. all: 16387 / Num. obs: 16387 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 23 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QB0 Resolution: 2→35.44 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 431894.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.4377 Å2 / ksol: 0.373336 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→35.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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