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- PDB-1qf8: TRUNCATED FORM OF CASEIN KINASE II BETA SUBUNIT (2-182) FROM HOMO... -

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Basic information

Entry
Database: PDB / ID: 1qf8
TitleTRUNCATED FORM OF CASEIN KINASE II BETA SUBUNIT (2-182) FROM HOMO SAPIENS
ComponentsCASEIN KINASE II
KeywordsTRANSFERASE / CASEIN KINASE BETA SUBUNIT (1-182) / SER/THR PROTEIN KINASE / ZN FINGER
Function / homology
Function and homology information


regulation of DNA binding / positive regulation of activin receptor signaling pathway / adiponectin-activated signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / protein kinase regulator activity / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body ...regulation of DNA binding / positive regulation of activin receptor signaling pathway / adiponectin-activated signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / protein kinase regulator activity / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / peptidyl-threonine phosphorylation / Signal transduction by L1 / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / fibrillar center / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / protein-containing complex assembly / protein-macromolecule adaptor activity / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / ficolin-1-rich granule lumen / protein domain specific binding / signaling receptor binding / negative regulation of cell population proliferation / protein serine/threonine kinase activity / chromatin binding / Neutrophil degranulation / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytosol / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsChantalat, L. / Leroy, D. / Filhol, O. / Nueda, A. / Benitez, M.J. / Chambaz, E. / Cochet, C. / Dideberg, O.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of the human protein kinase CK2 regulatory subunit reveals its zinc finger-mediated dimerization.
Authors: Chantalat, L. / Leroy, D. / Filhol, O. / Nueda, A. / Benitez, M.J. / Chambaz, E.M. / Cochet, C. / Dideberg, O.
History
DepositionApr 7, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CASEIN KINASE II
B: CASEIN KINASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2615
Polymers43,1062
Non-polymers1553
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.230, 132.230, 63.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

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Components

#1: Protein CASEIN KINASE II


Mass: 21552.885 Da / Num. of mol.: 2 / Fragment: BETA SUBUNIT (RESIDUES 1-182)
Source method: isolated from a genetically manipulated source
Details: TRUNCATED, CONTAINS RESIDUES 1-182 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P67870, EC: 2.7.1.37
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsZINC FINGER
Sequence detailsRESIDUES 183-215 HAVE BEEN DELETED

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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: 2.7 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 9
Details: CRYSTALS OF CK2 BETA (1-182) WERE GROWN AT 281 K IN 4 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (18 MG/ML) IN 10 MM TRIS (PH 7) AND RESERVOIR SOLUTION WITH 15% ...Details: CRYSTALS OF CK2 BETA (1-182) WERE GROWN AT 281 K IN 4 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (18 MG/ML) IN 10 MM TRIS (PH 7) AND RESERVOIR SOLUTION WITH 15% PEG 5K MME, 500 MM NACL, 460 MM MGCL2 3% DIOXANE, pH 9, VAPOR DIFFUSION, SITTING DROP
Crystal
*PLUS
Crystal grow
*PLUS
pH: 9.2 / Method: vapor diffusion, hanging drop / Details: Chantalat, L., (1999) Acta Crystallogr., D55, 895.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
214-20 %mPEG50001reservoir
40.46 M1reservoirMgCl2
510 mMdithiothreitol1reservoir
63 %dioxane1reservoir
70.4 M1reservoirNaCl
3bicine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.88, 0.978668, 0.978418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.881
20.9786681
30.9784181
ReflectionResolution: 1.7→30 Å / Num. obs: 634684 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 34
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 10 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 7.05 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 62119 / Num. measured all: 634684
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
SOLOMONphasing
CNS0.4refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.74→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2101218.05 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5818 10 %RANDOM
Rwork0.194 ---
obs-57967 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.66 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2--2.08 Å20 Å2
3----4.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 3 324 3031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.781.5
X-RAY DIFFRACTIONc_mcangle_it1.32
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 1.74→1.85 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 958 10 %
Rwork0.226 8605 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.1933
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / % reflection Rfree: 10 % / Rfactor Rwork: 0.226

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