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- PDB-6l23: Crystal structure of CK2a1 V116I with hematein -

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Basic information

Entry
Database: PDB / ID: 6l23
TitleCrystal structure of CK2a1 V116I with hematein
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase / 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 / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...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 / 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 signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / 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
Similarity search - Domain/homology
Chem-E3U / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9744942746 Å
AuthorsTsuyuguchi, M. / Kinoshita, T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Structural insights for producing CK2 alpha 1-specific inhibitors.
Authors: Tsuyuguchi, M. / Nakaniwa, T. / Hirasawa, A. / Nakanishi, I. / Kinoshita, T.
History
DepositionOct 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,35111
Polymers40,4921
Non-polymers85910
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint28 kcal/mol
Surface area16180 Å2
Unit cell
Length a, b, c (Å)51.861, 79.021, 79.775
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 40492.219 Da / Num. of mol.: 1 / Mutation: V116I
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-E3U / (6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one


Mass: 300.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Ethylene glycol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 23632 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 18.5570689193 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 50.3
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 0.65 / Num. unique obs: 2214

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 1.9744942746→38.0945946612 Å / SU ML: 0.174841527513 / Cross valid method: FREE R-VALUE / σ(F): 1.3518212696 / Phase error: 21.660456986
RfactorNum. reflection% reflection
Rfree0.228733919588 1212 5.14060313017 %
Rwork0.179110694155 --
obs0.181669755913 23577 99.586061246 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.9822130972 Å2
Refinement stepCycle: LAST / Resolution: 1.9744942746→38.0945946612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 30 117 2992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007579551974022981
X-RAY DIFFRACTIONf_angle_d1.109888695394025
X-RAY DIFFRACTIONf_chiral_restr0.0451705550116408
X-RAY DIFFRACTIONf_plane_restr0.00477692708643509
X-RAY DIFFRACTIONf_dihedral_angle_d13.86976746351117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9745-2.05350.2462142681791170.1714035913492417X-RAY DIFFRACTION97.762345679
2.0535-2.1470.2567297189291450.1628455771812436X-RAY DIFFRACTION100
2.147-2.26020.221224461461450.1635240371852455X-RAY DIFFRACTION100
2.2602-2.40180.2617790112011280.1764067872472445X-RAY DIFFRACTION100
2.4018-2.58720.2212363228211390.1755759310332471X-RAY DIFFRACTION100
2.5872-2.84740.2340406194211260.1843058726922499X-RAY DIFFRACTION100
2.8474-3.25930.2328463309541460.1862769608572495X-RAY DIFFRACTION100
3.2593-4.10560.2049296523011310.17317757482530X-RAY DIFFRACTION100
4.1056-38.090.225632824781350.1919046354742617X-RAY DIFFRACTION98.5673352436

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