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Yorodumi- PDB-1f0q: CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF PROTEIN KINASE CK2 IN C... -
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-Basic information
Entry | Database: PDB / ID: 1f0q | ||||||
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Title | CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF PROTEIN KINASE CK2 IN COMPLEX WITH THE NUCLEOTIDE COMPETITIVE INHIBITOR EMODIN | ||||||
Components | PROTEIN KINASE CK2, ALPHA SUBUNITCasein kinase 2 | ||||||
Keywords | TRANSFERASE / protein kinase-inhibitor complex | ||||||
Function / homology | Function and homology information protein kinase CK2 complex / regulation of cell cycle / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.63 Å | ||||||
Authors | Battistutta, R. / Sarno, S. / De Moliner, E. / Papinutto, E. / Zanotti, G. / Pinna, L.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: The replacement of ATP by the competitive inhibitor emodin induces conformational modifications in the catalytic site of protein kinase CK2. Authors: Battistutta, R. / Sarno, S. / De Moliner, E. / Papinutto, E. / Zanotti, G. / Pinna, L.A. #1: Journal: Embo J. / Year: 1998 Title: Crystal Structure of the Catalitic Subunit of Protein Kinase CK2 from Zea mays at 2.1 A Resolution Authors: Niefind, K. / Guerra, B. / Pinna, L.A. / Issinger, O.G. / Schomburg, D. #2: Journal: Nat.Struct.Biol. / Year: 1999 Title: GTP Plus Water Mimic ATP in the Active Site of Protein Kinase CK2 Authors: Niefind, K. / Putter, M. / Guerra, B. / Issinger, O.G. / Schomburg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f0q.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f0q.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 1f0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/1f0q ftp://data.pdbj.org/pub/pdb/validation_reports/f0/1f0q | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 39291.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: P28523, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-EMO / |
#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: 2.1 Å3/Da / Density % sol: 41.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 4000, sodium acetate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 Details: Guerra, B., (1998) Acta Crystallogr., Sect.D, 54, 143. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 21, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→25.7 Å / Num. all: 8792 / Num. obs: 8792 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.63→2.77 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.156 / % possible all: 83.6 |
Reflection | *PLUS Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 83.6 % / Num. unique obs: 1186 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Resolution: 2.63→24.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000812.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.8316 Å2 / ksol: 0.343965 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.63→24.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.63→2.79 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.7 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 50.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.357 / % reflection Rfree: 10.9 % / Rfactor Rwork: 0.271 |