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Yorodumi- PDB-1lpu: Low Temperature Crystal Structure of the Apo-form of the catalyti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lpu | ||||||
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Title | Low 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 / FOURIER SYNTHESIS / Resolution: 1.86 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 | 1lpu.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpu.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpu ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpu | HTTPS FTP |
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-Related structure data
Related structure data | 1lp4C 1lr4C 3juhC 1a6o 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 / Production host: Escherichia coli (E. coli) / 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.47 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: PEG3350, Tris/HCl, sodium acetate, 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: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 20, 1998 / Details: double mirrors |
Radiation | Monochromator: Ni-filter + double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→69.6 Å / Num. all: 31554 / Num. obs: 31230 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.084 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.86→1.92 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4 / Num. unique all: 2845 / Rsym value: 0.473 / % possible all: 89.8 |
Reflection | *PLUS Lowest resolution: 69 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 89.8 % / Rmerge(I) obs: 0.473 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1a6o 1a6o Resolution: 1.86→69.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.151 / 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: 22.307 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→69.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.858→1.906 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 69 Å / Rfactor obs: 0.204 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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