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- PDB-1na7: Crystal structure of the catalytic subunit of human protein kinase CK2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1na7 | ||||||
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Title | Crystal structure of the catalytic subunit of human protein kinase CK2 | ||||||
![]() | Casein kinase II, alpha chain | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pechkova, E. / Zanotti, G. / Nicolini, C. | ||||||
![]() | ![]() Title: Three-dimensional atomic structure of a catalytic subunit mutant of human protein kinase CK2. Authors: Pechkova, E. / Zanotti, G. / Nicolini, C. #1: ![]() Title: Crystal structure of the catalytic 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: ![]() Title: Structural features underlying selective inhibition of protein kinase CK2 by ATP site-directed tetrabromo-2-benzotriazole Authors: Battistutta, R. / De Moliner, E. / Sarno, S. / Zanotti, G. / Pinna, L.A. #3: ![]() Title: Accelerated protein crystal growth by protein thin film template Authors: Pechkova, E. / Nicolini, C. #4: ![]() Title: Protein nucleation and crystallization by homologous protein thin film template Authors: Pechkova, E. / Nicolini, C. #5: ![]() Title: From art to science in protein crystallization by means of thin-film technology Authors: Pechkova, E. / Nicolini, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.1 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m2rS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39333.895 Da / Num. of mol.: 1 / Fragment: Catalytic subunit / Mutation: E27A, K76N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.54 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: lb modified hanging drop method / pH: 8 Details: PEG 3500, NaAC, Tris, pH 8, LB Modified hanging drop method, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 10, 2002 / Details: microfocus |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→29.21 Å / Num. all: 12457 / Num. obs: 12457 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1817 / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 29 Å / % possible obs: 99 % |
Reflection shell | *PLUS % possible obs: 99.4 % / Num. unique obs: 1817 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1M2R Resolution: 2.4→29.21 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.8231 Å2 / ksol: 0.360107 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 29 Å / Num. reflection obs: 12457 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.53 Å / Rfactor Rfree: 0.03 / Num. reflection Rwork: 1817 |