[English] 日本語
Yorodumi- PDB-1ymd: Crystal Structure of the CDC25B phosphatase catalytic domain with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ymd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfonic 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: 1.7 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ymd.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ymd.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ymd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ymd_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ymd_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 1ymd_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1ymd_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1ymd ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1ymd | HTTPS FTP |
-Related structure data
Related structure data | 1ym9C 1ymkC 1ymlC 1ys0C 1qb0S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20729.801 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 |
---|---|
#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.6 % |
---|---|
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 |
---|---|
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: 1.7→35.74 Å / Num. all: 28852 / Num. obs: 28852 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.1 Å2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QB0 Resolution: 1.7→35.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 254602 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.2853 Å2 / ksol: 0.370394 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.74 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|