[English] 日本語
Yorodumi- PDB-3op3: Crystal Structure of Cell Division Cycle 25C Protein Isoform A fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3op3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Cell Division Cycle 25C Protein Isoform A from Homo sapiens | ||||||
Components | M-phase inducer phosphatase 3 | ||||||
Keywords | HYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / alpha-beta-alpha sandwich / kinase / cytosol | ||||||
Function / homology | Function and homology information positive regulation of G2/MI transition of meiotic cell cycle / WW domain binding / Polo-like kinase mediated events / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of mitotic nuclear division / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of cyclin-dependent protein serine/threonine kinase activity / phosphoprotein phosphatase activity / Activation of ATR in response to replication stress / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...positive regulation of G2/MI transition of meiotic cell cycle / WW domain binding / Polo-like kinase mediated events / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of mitotic nuclear division / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of cyclin-dependent protein serine/threonine kinase activity / phosphoprotein phosphatase activity / Activation of ATR in response to replication stress / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / RHO GTPases activate PKNs / positive regulation of G2/M transition of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitochondrial intermembrane space / G2/M transition of mitotic cell cycle / spermatogenesis / cell population proliferation / cell division / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Kim, Y. / Weger, A. / Hatzos, C. / Savitsky, P. / Johansson, C. / Ball, L. / Barr, A. / Vollmar, M. / Muniz, J. / Weigelt, J. ...Kim, Y. / Weger, A. / Hatzos, C. / Savitsky, P. / Johansson, C. / Ball, L. / Barr, A. / Vollmar, M. / Muniz, J. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. / von Delft, F. / Knapp, S. / Joachimiak, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of Cell Division Cycle 25C Protein Isoform A from Homo sapiens Authors: Kim, Y. / Weger, A. / Hatzos, C. / Savitsky, P. / Johansson, C. / Ball, L. / Barr, A. / Vollmar, M. / Muniz, J. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. / ...Authors: Kim, Y. / Weger, A. / Hatzos, C. / Savitsky, P. / Johansson, C. / Ball, L. / Barr, A. / Vollmar, M. / Muniz, J. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. / von Delft, F. / Knapp, S. / Joachimiak, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3op3.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3op3.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 3op3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/3op3 ftp://data.pdbj.org/pub/pdb/validation_reports/op/3op3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ifvS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25407.881 Da / Num. of mol.: 1 / Fragment: UNP residues 270-462 Source method: isolated from a genetically manipulated source Details: Cleavable N-terminal His6 tag / Source: (gene. exp.) Homo sapiens (human) / Gene: CDC25C / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P30307, protein-tyrosine-phosphatase | ||
---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.75 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Bis Tris pH 5.5, 23% PEG 3350, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→50 Å / Num. all: 9980 / Num. obs: 9980 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 78 Å2 / Rsym value: 0.097 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.63→2.68 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 437 / Rsym value: 0.759 / % possible all: 87.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID 2IFV Resolution: 2.63→49.31 Å / Cor.coef. Fo:Fc: 0.9391 / Cor.coef. Fo:Fc free: 0.9338 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.16 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.431 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.63→49.31 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.63→2.94 Å / Total num. of bins used: 5
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
|