+Open data
-Basic information
Entry | Database: PDB / ID: 1qb0 | ||||||
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Title | HUMAN CDC25B CATALYTIC DOMAIN | ||||||
Components | PROTEIN (M-PHASE INDUCER PHOSPHATASE 2 (CDC25B)) | ||||||
Keywords | HYDROLASE / CELL CYCLE PHOSPHATASE / DUAL SPECIFICITY PROTEIN PHOSPHATASE / CDC25 / CDC25B | ||||||
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 / MIR / Resolution: 1.91 Å | ||||||
Authors | Watenpaugh, K.D. / Reynolds, R.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of the catalytic subunit of Cdc25B required for G2/M phase transition of the cell cycle. Authors: Reynolds, R.A. / Yem, A.W. / Wolfe, C.L. / Deibel Jr., M.R. / Chidester, C.G. / Watenpaugh, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qb0.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qb0.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 1qb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qb0_validation.pdf.gz | 386.4 KB | Display | wwPDB validaton report |
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Full document | 1qb0_full_validation.pdf.gz | 388.1 KB | Display | |
Data in XML | 1qb0_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1qb0_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/1qb0 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/1qb0 | HTTPS FTP |
-Related 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: 24907.461 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: CDC25B / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P30305, protein-tyrosine-phosphatase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: 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: 2.68 Å3/Da / Density % sol: 54.16 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 4 MICROLITERS PROTEIN (10 MG/ML IN 50 MM TRISHCL, 1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C, VAPOR DIFFUSION, ...Details: 4 MICROLITERS PROTEIN (10 MG/ML IN 50 MM TRISHCL, 1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 29, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→20 Å / Num. all: 21239 / Num. obs: 21239 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.4 / % possible all: 55.7 |
Reflection | *PLUS Num. measured all: 76415 |
Reflection shell | *PLUS % possible obs: 55.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.91→10 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.91→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 4 / Num. reflection Rfree: 909 / Rfactor Rfree: 0.178 / Rfactor Rwork: 0.135 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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