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Yorodumi- PDB-1lr4: Room Temperature Crystal Structure of the Apo-form of the catalyt... -
+Open data
-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 | |||||||||
Components | Protein kinase CK2Casein kinase 2 | |||||||||
Keywords | TRANSFERASE / protein kinase / CK2 / casein kinase 2 / dual-cosubstrate specificity | |||||||||
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: 2 Å | |||||||||
Authors | Niefind, K. / Puetter, M. / Guerra, B. / Issinger, O.-G. / Schomburg, D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 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: 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. #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: Journal: Embo J. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lr4.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lr4.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lr4 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lr4 | HTTPS FTP |
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-Related structure data
Related structure data | 1lp4C 1lpuC 3juhC 1hclS C: citing same article (ref.) S: Starting model for refinement |
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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 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.) Zea mays (maize) / Plasmid: pt7-7 / 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-BEN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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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: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |