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Yorodumi- PDB-1ckj: CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ckj | ||||||
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Title | CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317 COMPLEX WITH BOUND TUNGSTATE | ||||||
Components | RECOMBINANT CASEIN KINASE I DELTA | ||||||
Keywords | PHOSPHOTRANSFERASE / PROTEIN KINASE | ||||||
Function / homology | Function and homology information Major pathway of rRNA processing in the nucleolus and cytosol / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / positive regulation of non-canonical Wnt signaling pathway / COPII-mediated vesicle transport ...Major pathway of rRNA processing in the nucleolus and cytosol / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / positive regulation of non-canonical Wnt signaling pathway / COPII-mediated vesicle transport / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / tau-protein kinase activity / Golgi organization / positive regulation of Wnt signaling pathway / spindle assembly / cellular response to nerve growth factor stimulus / ciliary basal body / spindle microtubule / regulation of circadian rhythm / circadian regulation of gene expression / Wnt signaling pathway / spindle / positive regulation of canonical Wnt signaling pathway / endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.46 Å | ||||||
Authors | Longenecker, K.L. / Roach, P.J. / Hurley, T.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Three-dimensional structure of mammalian casein kinase I: molecular basis for phosphate recognition. Authors: Longenecker, K.L. / Roach, P.J. / Hurley, T.D. #1: Journal: Embo J. / Year: 1995 Title: Crystal Structure of Casein Kinase-1, a Phosphate-Directed Protein Kinase Authors: Xu, R. / Carmel, G. / Sweet, R.M. / Kuret, J. / Cheng, X. #2: Journal: J.Biol.Chem. / Year: 1993 Title: Molecular Cloning, Expression, and Characterization of a 49-Kilodalton Casein Kinase I Isoform from Rat Testis Authors: Graves, P.R. / Haas, D.W. / Hagedorn, C.H. / Depaoli-Roach, A.A. / Roach, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ckj.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ckj.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ckj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ckj_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
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Full document | 1ckj_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | 1ckj_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 1ckj_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1ckj ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1ckj | 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: 36995.531 Da / Num. of mol.: 2 Mutation: C-TERMINAL TRUNCATION MUTANT CONTAINING RESIDUES 1 - 317 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: HOST BL21(DE3) / Cell line: 293 / Gene: T7 / Organ: TESTES / Plasmid: PET-8C / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 References: UniProt: Q06486, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | ChemComp-WO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.25 % | ||||||||||||||||||||
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Crystal grow | Details: MOLECULE: RECOMBINANT CASEIN KINASE I DELTA. CRYSTALS WERE GROWN BY THE SITTING DROP TECHNIQUE, MIXING 3 MICROLITER OF PROTEIN SOLUTION WITH 3 MICROLITER OF RESERVOIR SOLUTION. THE PROTEIN ...Details: MOLECULE: RECOMBINANT CASEIN KINASE I DELTA. CRYSTALS WERE GROWN BY THE SITTING DROP TECHNIQUE, MIXING 3 MICROLITER OF PROTEIN SOLUTION WITH 3 MICROLITER OF RESERVOIR SOLUTION. THE PROTEIN SOLUTION CONSISTED OF 14 MG/ML PROTEIN IN 50 MM TRIS-HCL (PH=7.5), 1 MM EDTA, 5 MM DTT, 0.2 M NACL, 2.5 MM BETA-OCTYL GLUCOSIDE. THE RESERVOIR SOLUTION CONTAINED 15% PEG 3400, 50 MM SODIUM CITRATE, 50 MM DIBASIC POTASSIUM PHOSPHATE, (PH=6.8). DATA WAS COLLECTED ON A CRYSTAL SOAKED FOR 6 DAYS IN 15% PEG 3400, 50 MM SODIUM CITRATE, 17.5 MM SODIUM TUNGSTATE, (PH=6.8). ROOM TEMPERATURE. | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 51 % | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→53 Å / Num. obs: 23846 / % possible obs: 85 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Num. measured all: 70215 / Rmerge(I) obs: 0.066 |
-Processing
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Refinement | Resolution: 2.46→8 Å / σ(F): 1
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Displacement parameters | Biso mean: 38.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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