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Yorodumi- PDB-2ifv: Crystal structure of an active site mutant, C473D, of CDC25B phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ifv | ||||||
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Title | Crystal structure of an active site mutant, C473D, of CDC25B phosphatase catalytic domain | ||||||
Components | M-phase inducer phosphatase 2 | ||||||
Keywords | HYDROLASE / PHOSPHATASE / DUAL SPECIFICITY / ACTIVE SITE MUTANT | ||||||
Function / homology | Function and homology information positive regulation of G2/MI transition of meiotic cell cycle / oocyte maturation / female meiosis I / 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 / oocyte maturation / female meiosis I / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Rudolph, J. / Buhrman, G. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Kinetic and structural studies of specific protein-protein interactions in substrate catalysis by Cdc25B phosphatase. Authors: Sohn, J. / Buhrman, G. / Rudolph, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ifv.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ifv.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ifv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/2ifv ftp://data.pdbj.org/pub/pdb/validation_reports/if/2ifv | HTTPS FTP |
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-Related structure data
Related structure data | 2ifdC 1ymkS 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: 20693.746 Da / Num. of mol.: 1 / Fragment: Catalytic domain, residues 391-564 / Mutation: C473D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC25B, CDC25HU2 / Plasmid: PET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30305, protein-tyrosine-phosphatase | ||
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#2: Chemical | #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: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: DTT, AMMONIUM SULFATE, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-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: 1.6→30 Å / Num. all: 35424 / Num. obs: 34010 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 32.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YMK Resolution: 1.6→29.69 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 243843.01 / 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: 46.4737 Å2 / ksol: 0.374661 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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