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- PDB-5ywm: Crystal structure of CK2a2 form-1 -

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Basic information

Entry
Database: PDB / ID: 5ywm
TitleCrystal structure of CK2a2 form-1
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / Protein kinase
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: 1.939 Å
AuthorsTsuyuguchi, M. / Kinoshita, T.
CitationJournal: To Be Published
Title: Crystal structure of human CK2a2 in a new crystal form at 1.89 angstrom resolution
Authors: Tsuyuguchi, M. / Nakaniwa, T. / Kinoshita, T.
History
DepositionNov 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4754
Polymers40,1601
Non-polymers3153
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-15 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.292, 101.023, 45.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 40159.984 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.06 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: PEG 4000, Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.939→50 Å / Num. obs: 44654 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.97
Reflection shellResolution: 1.939→2.06 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.637 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E3B

3e3b


Resolution: 1.939→45.764 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 3772 8.46 %
Rwork0.1907 --
obs0.1952 44583 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.939→45.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 19 142 2799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082751
X-RAY DIFFRACTIONf_angle_d1.0963713
X-RAY DIFFRACTIONf_dihedral_angle_d15.1121034
X-RAY DIFFRACTIONf_chiral_restr0.046386
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9391-1.96370.53041310.45811443X-RAY DIFFRACTION95
1.9637-1.98950.35511400.29051545X-RAY DIFFRACTION100
1.9895-2.01680.30971360.24891477X-RAY DIFFRACTION100
2.0168-2.04560.29381370.24981499X-RAY DIFFRACTION100
2.0456-2.07610.291430.22271539X-RAY DIFFRACTION100
2.0761-2.10850.25481390.22891519X-RAY DIFFRACTION100
2.1085-2.14310.25131340.22821503X-RAY DIFFRACTION100
2.1431-2.18010.30451460.22621549X-RAY DIFFRACTION100
2.1801-2.21970.29261360.20841470X-RAY DIFFRACTION100
2.2197-2.26240.28251430.21781560X-RAY DIFFRACTION100
2.2624-2.30860.27841440.22211504X-RAY DIFFRACTION100
2.3086-2.35880.311380.22481493X-RAY DIFFRACTION100
2.3588-2.41360.28221480.21181545X-RAY DIFFRACTION100
2.4136-2.4740.26331310.21991491X-RAY DIFFRACTION100
2.474-2.54090.31711440.211525X-RAY DIFFRACTION100
2.5409-2.61560.2831360.20671496X-RAY DIFFRACTION100
2.6156-2.70010.28771470.20881549X-RAY DIFFRACTION100
2.7001-2.79650.27741380.19991470X-RAY DIFFRACTION100
2.7965-2.90850.25421430.21161540X-RAY DIFFRACTION100
2.9085-3.04080.28381380.2131502X-RAY DIFFRACTION100
3.0408-3.20110.23141380.20311495X-RAY DIFFRACTION100
3.2011-3.40160.26931400.18361522X-RAY DIFFRACTION100
3.4016-3.66420.24611340.17321522X-RAY DIFFRACTION100
3.6642-4.03270.18481440.15521514X-RAY DIFFRACTION100
4.0327-4.61580.18811400.1481525X-RAY DIFFRACTION100
4.6158-5.81350.20111430.16121516X-RAY DIFFRACTION100
5.8135-45.77670.19981410.1691498X-RAY DIFFRACTION99

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