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- PDB-2r7i: Crystal structure of catalytic subunit of protein kinase CK2 -

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Basic information

Entry
Database: PDB / ID: 2r7i
TitleCrystal structure of catalytic subunit of protein kinase CK2
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / catalytic subunit / kinase / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase / Wnt signaling pathway
Function / homology
Function and homology information


WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Receptor Mediated Mitophagy / Synthesis of PC / Regulation of PTEN stability and activity / Regulation of TP53 Activity through Phosphorylation / Signal transduction by L1 / PcG protein complex / protein phosphatase regulator activity ...WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Receptor Mediated Mitophagy / Synthesis of PC / Regulation of PTEN stability and activity / Regulation of TP53 Activity through Phosphorylation / Signal transduction by L1 / PcG protein complex / protein phosphatase regulator activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / regulation of chromosome separation / positive regulation of aggrephagy / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Sin3-type complex / response to testosterone / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / ribonucleoprotein complex binding / regulation of protein localization to plasma membrane / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / liver regeneration / beta-catenin binding / PML body / cerebral cortex development / Wnt signaling pathway / positive regulation of protein catabolic process / kinase activity / rhythmic process / double-strand break repair / positive regulation of cell growth / 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 / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / chromatin / ATP binding / identical protein 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
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsShen, Y.
CitationJournal: CHIN.SCI.BULL. / Year: 2009
Title: Crystal structures of catalytic and regulatory subunits of rat protein kinase CK2
Authors: Zhou, W. / Qin, X. / Yan, X. / Xie, X. / Li, L. / Fang, S. / Long, J. / Adelman, J. / Tang, W.-J. / Shen, Y.
History
DepositionSep 8, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Casein kinase II subunit alpha
C: Casein kinase II subunit alpha
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,15612
Polymers160,3874
Non-polymers7698
Water55831
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2893
Polymers40,0971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2893
Polymers40,0971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2893
Polymers40,0971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2893
Polymers40,0971
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.517, 127.517, 126.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )A2 - 44
121CHAIN A AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )A53 - 103
131CHAIN A AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )A108 - 330
211CHAIN B AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )B2 - 44
221CHAIN B AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )B53 - 103
231CHAIN B AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )B108 - 330
311CHAIN C AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )C2 - 44
321CHAIN C AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )C53 - 103
331CHAIN C AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )C108 - 330
411CHAIN D AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )D2 - 44
421CHAIN D AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )D53 - 103
431CHAIN D AND (RESSEQ 2:44 OR RESSEQ 53:103 OR RESSEQ 108:330 )D108 - 330

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Components

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


Mass: 40096.770 Da / Num. of mol.: 4 / Fragment: catalytic subunit, C-terminal truncation 1-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CK2 / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P19139, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Li2SO4, PEG 3350, Bis-Tris buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 40253 / Num. obs: 40213 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 41.99 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.11 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.85 / Rsym value: 0.551 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.003→19.574 Å / SU ML: 0.38 / Isotropic thermal model: RESTRAINED / σ(F): 0.08 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1935 5.04 %
Rwork0.2161 --
obs0.2181 38373 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.392 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.22 Å20 Å20 Å2
2--5.22 Å20 Å2
3----10.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3.003→19.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10748 0 40 31 10819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611062
X-RAY DIFFRACTIONf_angle_d0.93414972
X-RAY DIFFRACTIONf_dihedral_angle_d18.6444006
X-RAY DIFFRACTIONf_chiral_restr0.0671575
X-RAY DIFFRACTIONf_plane_restr0.0031913
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2655X-RAY DIFFRACTIONPOSITIONAL0.031
12B2655X-RAY DIFFRACTIONPOSITIONAL0.031
13C2663X-RAY DIFFRACTIONPOSITIONAL0.012
14D2663X-RAY DIFFRACTIONPOSITIONAL0.031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.003-3.07780.34731250.28132261X-RAY DIFFRACTION84
3.0778-3.16070.30441260.25842430X-RAY DIFFRACTION89
3.1607-3.25330.27641520.23592520X-RAY DIFFRACTION93
3.2533-3.35780.27921440.21982610X-RAY DIFFRACTION96
3.3578-3.47720.21891510.21072604X-RAY DIFFRACTION97
3.4772-3.61550.28041470.20592613X-RAY DIFFRACTION96
3.6155-3.7790.26381430.20412638X-RAY DIFFRACTION97
3.779-3.97660.22921270.20242627X-RAY DIFFRACTION96
3.9766-4.22350.23831290.18232652X-RAY DIFFRACTION97
4.2235-4.54580.21911320.18572691X-RAY DIFFRACTION98
4.5458-4.99630.21221290.17122690X-RAY DIFFRACTION98
4.9963-5.70360.23631560.20072663X-RAY DIFFRACTION98
5.7036-7.12780.2571290.23672709X-RAY DIFFRACTION98
7.1278-19.57410.27791450.23742730X-RAY DIFFRACTION98
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4.paramso4.top

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