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- PDB-5kwh: Crystal structure of CK2 -

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Basic information

Entry
Database: PDB / ID: 5kwh
TitleCrystal structure of CK2
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / CK2 / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / 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 ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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-6XT / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsFerguson, A.D.
CitationJournal: To Be Published
Title: Crystal structure of CK2
Authors: Ferguson, A.D.
History
DepositionJul 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,16841
Polymers79,7572
Non-polymers3,41139
Water6,810378
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,75623
Polymers39,8781
Non-polymers1,87822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,41218
Polymers39,8781
Non-polymers1,53317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Casein kinase II subunit alpha
hetero molecules

B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,16841
Polymers79,7572
Non-polymers3,41139
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z+1/41
Buried area6620 Å2
ΔGint-173 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.170, 126.170, 124.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 39878.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-6XT / ~{N}-[5-[[7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]ethanamide


Mass: 336.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 22-26% PEG 6K, 200 mM ammonium sulfate, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→126.8 Å / Num. obs: 57725 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 34.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.277 / Net I/σ(I): 12.9
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 16.2 % / Mean I/σ(I) obs: 2.3 / CC1/2: 0.997 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5h8b

5h8b


Resolution: 2.12→31.04 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.173 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2877 5 %RANDOM
Rwork0.181 ---
obs0.182 57518 100 %-
Displacement parametersBiso mean: 35.54 Å2
Baniso -1Baniso -2Baniso -3
1--3.9415 Å20 Å20 Å2
2---3.9415 Å20 Å2
3---7.883 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 2.12→31.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 211 378 6175
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015925HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.987977HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2089SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes833HARMONIC5
X-RAY DIFFRACTIONt_it5925HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion19.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion695SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6954SEMIHARMONIC4
LS refinement shellResolution: 2.12→2.17 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 215 5.13 %
Rwork0.221 3973 -
all0.222 4188 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54-0.4533-0.15621.0764-0.30720.59680.03150.0129-0.0007-0.0801-0.00080.0681-0.0438-0.0327-0.0307-0.04970.0299-0.0115-0.0758-0.0105-0.0956-22.2727-53.81339.1879
21.18320.3867-0.28260.58690.00970.757-0.01070.03240.0292-0.02380.0017-0.0177-0.06960.02950.009-0.0446-0.0162-0.0262-0.10020.0103-0.09888.0203-41.69149.4534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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