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- PDB-1lr4: Room Temperature Crystal Structure of the Apo-form of the catalyt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lr4 | |||||||||
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Title | Room Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays | |||||||||
![]() | Protein kinase CK2 | |||||||||
![]() | TRANSFERASE / protein kinase / CK2 / casein kinase 2 / dual-cosubstrate specificity | |||||||||
Function / homology | ![]() protein kinase CK2 complex / regulation of cell cycle / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol 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 | ![]() | 88.6 KB | Display | ![]() |
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PDB format | ![]() | 66.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1lp4C ![]() 1lpuC ![]() 3juhC ![]() 1hclS C: citing same article ( 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 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 | ChemComp-BEN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG4000, sodium acetate, Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.1 / Details: used microseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 2, 1996 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→26.2 Å / Num. all: 25896 / Num. obs: 24342 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.106 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.7 % / Rsym value: 0.111 / % possible all: 84.9 |
Reflection | *PLUS Lowest resolution: 26 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.106 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 84.9 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 4.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: BACKBONE OF CYCLIN-DEPENDENT KINASE 2 (PDB entry 1HCL) Resolution: 2→26 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 27.212 Å2
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Refinement step | Cycle: LAST / Resolution: 2→26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Rfactor obs: 0.193 / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.05 Å / Rfactor obs: 0.216 |