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- PDB-3kxh: Crystal structure of Z. mays CK2 kinase alpha subunit in complex ... -

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Basic information

Entry
Database: PDB / ID: 3kxh
TitleCrystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor (2-dymethylammino-4,5,6,7-tetrabromobenzoimidazol-1yl-acetic acid (K66)
ComponentsCasein kinase II subunit alpha
KeywordsTransferase/Transferase inhibitor / Protein kinase CK2-inhibitor complex / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Transferase / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity ...protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-K66 / DI(HYDROXYETHYL)ETHER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body in an isomorphous cell / Resolution: 1.7 Å
AuthorsPapinutto, E. / Franchin, C. / Battistutta, R.
Citation
#1: 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.
#2: Journal: Chembiochem / Year: 2007
Title: The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules.
Authors: Battistutta, R. / Mazzorana, M. / Cendron, L. / Bortolato, A. / Sarno, S. / Kazimierczuk, Z. / Zanotti, G. / Moro, S. / Pinna, L.A.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3303
Polymers38,6891
Non-polymers6412
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.838, 60.411, 47.094
Angle α, β, γ (deg.)90.00, 103.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 38689.395 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-K66 / [4,5,6,7-tetrabromo-2-(dimethylamino)-1H-benzimidazol-1-yl]acetic acid


Mass: 534.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9Br4N3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2008 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→69.843 Å / Num. obs: 43218 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 12.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.537 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: Rigid body in an isomorphous cell
Resolution: 1.7→69.84 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.744 / SU ML: 0.091 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26648 2177 5 %RANDOM
Rwork0.21224 ---
obs0.21498 41038 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-0 Å2-0.99 Å2
2---0.58 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 27 248 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222838
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2691.9683839
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9685.06332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11923.767146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57715511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.441520
X-RAY DIFFRACTIONr_chiral_restr0.1760.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212169
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.461.51637
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.25822654
X-RAY DIFFRACTIONr_scbond_it3.66731201
X-RAY DIFFRACTIONr_scangle_it5.4794.51183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 165 -
Rwork0.305 3025 -
obs--99.94 %

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