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- PDB-1lp4: Crystal structure of a binary complex of the catalytic subunit of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lp4 | ||||||
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Title | Crystal structure of a binary complex of the catalytic subunit of protein kinase CK2 with Mg-AMPPNP | ||||||
![]() | Protein kinase CK2![]() | ||||||
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Function / homology | ![]() regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Niefind, K. / Puetter, M. / Guerra, B. / Issinger, O.-G. / Schomburg, D. | ||||||
![]() | ![]() Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate. Authors: Yde, C.W. / Ermakova, I. / Issinger, O.G. / Niefind, K. #1: Journal: Embo J. / Year: 1998 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: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Expression, purification and crystallization of the catalytic subunit of protein kinase CK2 from Zea mays Authors: Guerra, B. / Niefind, K. / Pinna, L.A. / Schomburg, D. / Issinger, O.-G. #3: ![]() 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. #4: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and preliminary characterization of crystals of human protein kinase CK2 Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.-G. #5: ![]() Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.-G. #6: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1993 Title: Expression and characterization of a recombinant maize CK-2 alpha subunit Authors: Boldyreff, B. / Meggio, F. / Dobrowolska, G. / Pinna, L.A. / Issinger, O.-G. #7: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1991 Title: Cloning and sequencing of the casein kinase 2 alpha subunit from Zea mays Authors: Dobrowolska, G. / Boldyreff, B. / Issinger, O.-G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.6 KB | Display | ![]() |
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PDB format | ![]() | 67.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-ANP / | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % | ||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: PEG3350, SODIUM ACETATE, TRIS/HCL, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: used microseeding | ||||||||||||||||||||||||
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: MACSCIENCE / Detector: IMAGE PLATE / Date: May 12, 1999 / Details: double mirrors |
Radiation | Monochromator: Ni-filters + double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.86→54.86 Å / Num. all: 31998 / Num. obs: 30598 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 26.1 Å2 / Rsym value: 0.054 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.86→1.92 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2435 / Rsym value: 0.552 / % possible all: 76.6 |
Reflection | *PLUS Lowest resolution: 55 Å / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 76.6 % / Rmerge(I) obs: 0.552 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.859→1.907 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 55 Å / Rfactor obs: 0.207 / Rfactor Rfree![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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