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- PDB-1om1: Crystal structure of maize CK2 alpha in complex with IQA -

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Basic information

Entry
Database: PDB / ID: 1om1
TitleCrystal structure of maize CK2 alpha in complex with IQA
ComponentsCasein kinase II, alpha chain
KeywordsTRANSFERASE / CK2 / IQA / inhibitor / Zea mays
Function / homology
Function and homology information


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
Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Chem-IQA / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsBattistutta, R. / De Moliner, E. / Zanotti, G.
CitationJournal: Biochem.J. / Year: 2003
Title: Biochemical and three-dimensional-structural study of the specific inhibition of protein kinase CK2 by [5-oxo-5,6-dihydroindolo-(1,2-a)quinazolin-7-yl]acetic acid (IQA).
Authors: Sarno, S. / de Moliner, E. / Ruzzene, M. / Pagano, M.A. / Battistutta, R. / Bain, J. / Fabbro, D. / Schoepfer, J. / Elliott, M. / Furet, P. / Meggio, F. / Zanotti, G. / Pinna, L.A.
History
DepositionFeb 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II, alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5832
Polymers39,2911
Non-polymers2921
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.524, 60.276, 44.546
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Casein kinase II, alpha chain / CK II / CK2-alpha


Mass: 39291.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: P28523, EC: 2.7.1.37
#2: Chemical ChemComp-IQA / (5-OXO-5,6-DIHYDRO-INDOLO[1,2-A]QUINAZOLIN-7-YL)-ACETIC ACID


Mass: 292.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, SODIUM ACETATE, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 283 K / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
2100 mMinhibitor solution1dropin 100%(v/v) DMSO
320 %(w/v)PEG40001reservoir
40.2 Msodium acetate1reservoir
50.1 MTris1reservoirpH8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 7, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.68→34.5 Å / Num. all: 41817 / Num. obs: 40418 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.9 Å2
Reflection shellResolution: 1.68→1.77 Å / % possible all: 85.6
Reflection
*PLUS
Num. obs: 41163 / % possible obs: 97.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 97.8 % / Redundancy: 2.6 % / Num. unique obs: 5404 / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→32.8 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3277 8.1 %RANDOM
Rwork0.206 ---
all-41817 --
obs-40418 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.3341 Å2 / ksol: 0.36169 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.03 Å20 Å2-0.01 Å2
2--12.19 Å20 Å2
3----5.16 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.68→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 44 252 3009
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.42
X-RAY DIFFRACTIONc_mcangle_it1.962.5
X-RAY DIFFRACTIONc_scbond_it2.312.5
X-RAY DIFFRACTIONc_scangle_it3.323
LS refinement shellResolution: 1.68→1.79 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 533 8.7 %
Rwork0.347 5618 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3IQA.PARAMIQA.TOP
Refinement
*PLUS
Num. reflection obs: 40448 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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