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Yorodumi- PDB-1m2r: Crystal structure of 5,8-di-amino-1,4-di-hydroxy-anthraquinone/CK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m2r | ||||||
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Title | Crystal structure of 5,8-di-amino-1,4-di-hydroxy-anthraquinone/CK2 kinase complex | ||||||
Components | CASEIN kinase II, alpha chain | ||||||
Keywords | TRANSFERASE / kinase / inhibitor-enzyme 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | De Moliner, E. / Moro, S. / Sarno, S. / Zagotto, G. / Zanotti, G. / Pinna, L.A. / Battistutta, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Inhibition of protein kinase CK2 by anthraquinone-related compounds. A structural insight Authors: De Moliner, E. / Sarno, S. / Moro, S. / Zanotti, G. / Battistutta, R. / Pinna, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m2r.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m2r.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 1m2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/1m2r ftp://data.pdbj.org/pub/pdb/validation_reports/m2/1m2r | HTTPS FTP |
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-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: 38673.395 Da / Num. of mol.: 1 / Fragment: catalytic subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P28523, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-MNY / |
#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: 2.085 Å3/Da / Density % sol: 41.07 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 4000, Sodium Acetate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID29 / Wavelength: 0.918 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 14, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.65 Å / Num. all: 35618 / Num. obs: 32030 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.097 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.7→1.81 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3069 / Rsym value: 0.156 / % possible all: 56.3 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 32021 / % possible obs: 89.7 % / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.79 Å / % possible obs: 55.2 % / Num. unique obs: 2851 / Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 1422813.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.6651 Å2 / ksol: 0.393209 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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