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- PDB-1na7: Crystal structure of the catalytic subunit of human protein kinase CK2 -

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Basic information

Entry
Database: PDB / ID: 1na7
TitleCrystal structure of the catalytic subunit of human protein kinase CK2
ComponentsCasein kinase II, alpha chain
KeywordsTRANSFERASE / CK2 / protein kinase / microcrystals / thin-film nanotechnology / microfocus ESRF
Function / homology
Function and homology information


: / regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex ...: / regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / rhythmic process / kinase activity / double-strand break repair / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / histone H2AS1 kinase activity / regulation of cell cycle / non-specific serine/threonine protein kinase / protein stabilization / negative regulation of translation / protein phosphorylation / protein serine/threonine kinase activity / protein serine kinase activity / positive regulation of cell population proliferation / DNA damage response / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPechkova, E. / Zanotti, G. / Nicolini, C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Three-dimensional atomic structure of a catalytic subunit mutant of human protein kinase CK2.
Authors: Pechkova, E. / Zanotti, G. / Nicolini, C.
#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: Protein Sci. / Year: 2001
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: Journal: J.CRYST.GROWTH / Year: 2001
Title: Accelerated protein crystal growth by protein thin film template
Authors: Pechkova, E. / Nicolini, C.
#4: Journal: J.Cell.Biochem. / Year: 2002
Title: Protein nucleation and crystallization by homologous protein thin film template
Authors: Pechkova, E. / Nicolini, C.
#5: Journal: Nanotechnology / Year: 2002
Title: From art to science in protein crystallization by means of thin-film technology
Authors: Pechkova, E. / Nicolini, C.
History
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II, alpha chain


Theoretical massNumber of molelcules
Total (without water)39,3341
Polymers39,3341
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.676, 45.954, 63.956
Angle α, β, γ (deg.)90.00, 111.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Casein kinase II, alpha chain / CK II


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.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68400, EC: 2.7.1.37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetails
125 %PEG35001drop
20.2 Msodium acetate1drop
30.1 MTris1droppH8.
425 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9755 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2002 / Details: microfocus
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M2R

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
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1277 10.3 %RANDOM
Rwork0.209 ---
all0.215 12448 --
obs0.215 12448 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.8231 Å2 / ksol: 0.360107 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.36 Å20 Å25.25 Å2
2--2.72 Å20 Å2
3---1.64 Å2
Refine analyzeLuzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 0 91 2848
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 216 10.4 %
Rwork0.245 1868 -
obs-1817 98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 29 Å / Num. reflection obs: 12457
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Lowest resolution: 2.53 Å / Rfactor Rfree: 0.03 / Num. reflection Rwork: 1817

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