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- PDB-2r6m: Crystal structure of rat CK2-beta subunit -

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Basic information

Entry
Database: PDB / ID: 2r6m
TitleCrystal structure of rat CK2-beta subunit
ComponentsCasein kinase II subunit beta
KeywordsMETAL BINDING PROTEIN / Zinc binding / regulatory subunit / Phosphorylation / 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 / positive regulation of activin receptor signaling pathway / adiponectin-activated signaling pathway / Regulation of TP53 Activity through Phosphorylation / Signal transduction by L1 ...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 / positive regulation of activin receptor signaling pathway / adiponectin-activated signaling pathway / Regulation of TP53 Activity through Phosphorylation / Signal transduction by L1 / endothelial tube morphogenesis / PcG protein complex / negative regulation of viral life cycle / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / protein kinase regulator activity / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Neutrophil degranulation / response to testosterone / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / ribonucleoprotein complex binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / liver regeneration / cell projection / PML body / Wnt signaling pathway / nuclear matrix / protein-macromolecule adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / protein domain specific binding / signaling receptor binding / protein serine/threonine kinase activity / chromatin binding / chromatin / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / N-terminal domain of TfIIb ...protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / N-terminal domain of TfIIb / Single Sheet / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Casein kinase II subunit beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,0704
Polymers49,9392
Non-polymers1312
Water70339
1
A: Casein kinase II subunit beta
hetero molecules

B: Casein kinase II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0704
Polymers49,9392
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/41
Buried area2210 Å2
ΔGint-18 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.010, 114.010, 73.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Casein kinase II subunit beta / regulatory subunit of protein kinase CK2 / CK II beta / Phosvitin


Mass: 24969.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pUBS520 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P67874
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaCl, PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 10169 / Num. obs: 10149 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.108 / Rsym value: 0.082 / Net I/σ(I): 27.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 14 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.511

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.73 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 98745.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 470 5.3 %RANDOM
Rwork0.239 ---
obs0.239 8864 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.7939 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 58.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.37 Å20 Å20 Å2
2--4.37 Å20 Å2
3----8.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 2 39 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it2.382.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 72 5.2 %
Rwork0.318 1307 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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