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- PDB-5yf9: Crystal structure of CK2a2 form-2 -

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Basic information

Entry
Database: PDB / ID: 5yf9
TitleCrystal structure of CK2a2 form-2
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / 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
NICOTINIC ACID / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsTsuyuguchi, M. / Kinoshita, T.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures of human CK2 alpha 2 in new crystal forms arising from a subtle difference in salt concentration
Authors: Tsuyuguchi, M. / Nakaniwa, T. / Kinoshita, T.
History
DepositionSep 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: 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
X: Casein kinase II subunit alpha'
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,33512
Polymers80,3202
Non-polymers1,01510
Water17,871992
1
X: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7637
Polymers40,1601
Non-polymers6036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-30 kcal/mol
Surface area14810 Å2
MethodPISA
2
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5715
Polymers40,1601
Non-polymers4114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.468, 102.422, 72.229
Angle α, β, γ (deg.)90.00, 95.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40159.984 Da / Num. of mol.: 2 / Fragment: UNP residues 1-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 992 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24%w/v PEG 4000, 0.15 M Lithium Sulfate mono hydrate, 0.1 M Tris-HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→46.289 Å / Num. obs: 53854 / % possible obs: 99.9 % / Redundancy: 1.8 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-20009data reduction
HKL-20009data scaling
MOLREP11.2.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OFM

3ofm


Resolution: 1.89→46.289 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 2733 5.08 %
Rwork0.2115 --
obs0.2142 53784 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→46.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 58 992 6430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085616
X-RAY DIFFRACTIONf_angle_d1.0587594
X-RAY DIFFRACTIONf_dihedral_angle_d14.1782112
X-RAY DIFFRACTIONf_chiral_restr0.043788
X-RAY DIFFRACTIONf_plane_restr0.006967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8899-1.92250.2951400.23072575X-RAY DIFFRACTION99
1.9225-1.95750.28451100.2412551X-RAY DIFFRACTION100
1.9575-1.99510.30771220.22872547X-RAY DIFFRACTION100
1.9951-2.03580.30671290.21832523X-RAY DIFFRACTION100
2.0358-2.08010.27631240.21242567X-RAY DIFFRACTION100
2.0801-2.12850.25971270.21362574X-RAY DIFFRACTION100
2.1285-2.18170.28051390.2172510X-RAY DIFFRACTION100
2.1817-2.24070.29021440.21972555X-RAY DIFFRACTION100
2.2407-2.30660.32551490.21382550X-RAY DIFFRACTION100
2.3066-2.38110.29481480.21812514X-RAY DIFFRACTION100
2.3811-2.46620.28341300.21292568X-RAY DIFFRACTION100
2.4662-2.56490.26841540.20842556X-RAY DIFFRACTION100
2.5649-2.68160.22731420.21362520X-RAY DIFFRACTION100
2.6816-2.8230.30681460.21662534X-RAY DIFFRACTION100
2.823-2.99980.27111470.21982555X-RAY DIFFRACTION100
2.9998-3.23140.25981270.21052560X-RAY DIFFRACTION100
3.2314-3.55650.24861490.19792560X-RAY DIFFRACTION100
3.5565-4.07080.23391470.18862546X-RAY DIFFRACTION100
4.0708-5.12780.21281400.19182592X-RAY DIFFRACTION100
5.1278-46.30330.24531190.23632594X-RAY DIFFRACTION99

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