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- PDB-2pvr: Crystal structure of the catalytic subunit of protein kinase CK2 ... -

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Basic information

Entry
Database: PDB / ID: 2pvr
TitleCrystal structure of the catalytic subunit of protein kinase CK2 (C-terminal deletion mutant 1-335) in complex with two sulfate ions
ComponentsCasein kinase II subunit alpha, catalytic subunit
KeywordsSIGNALING PROTEIN / TRANSFERASE / EUKARYOTIC PROTEIN KINASE FOLD / CMGC kinases
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / 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 / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.605 Å
AuthorsNiefind, K. / Yde, C.W. / Ermakova, I. / Issinger, O.-G.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Evolved to Be Active: Sulfate Ions Define Substrate Recognition Sites of CK2alpha and Emphasise its Exceptional Role within the CMGC Family of Eukaryotic Protein Kinases
Authors: Niefind, K. / Yde, C.W. / Ermakova, I. / Issinger, O.G.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit
Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.-G. / Niefind, K.
#2: Journal: Embo J. / Year: 2001
Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme
Authors: Niefind, K. / Guerra, B. / Ermakova, I. / Issinger, O.-G.
#3: Journal: J.Mol.Biol. / Year: 2005
Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
Authors: Yde, C.W. / Ermakova, I. / Issinger, O.-G. / Niefind, K.
History
DepositionMay 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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, catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6344
Polymers39,9361
Non-polymers6983
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.670, 45.371, 63.442
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe molecule occurs as a monomer

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Components

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


Mass: 39935.547 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3)
References: UniProt: P68400, 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEGmme 5000, ammonium sulfate, MES, adenylyl imidodiphosphate, magnesium chloride, peptide RRRADDSDDDDD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2003 / Details: Osmic multilayer mirror
RadiationMonochromator: Osmic multilayer mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.605→19.71 Å / Num. all: 40626 / Num. obs: 40464 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.142 / Net I/σ(I): 10.5
Reflection shellResolution: 1.605→1.7 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 5999 / Rsym value: 46.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.2refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PJK

1pjk


Resolution: 1.605→19.71 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.882 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.105 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24146 2034 5 %RANDOM
Rwork0.18396 ---
all0.1868 40666 --
obs0.1868 38632 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.33 Å2
2--0.19 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.605→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 41 310 3122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212924
X-RAY DIFFRACTIONr_bond_other_d0.0010.022025
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9623969
X-RAY DIFFRACTIONr_angle_other_deg0.87334882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15323.057157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49715511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.451526
X-RAY DIFFRACTIONr_chiral_restr0.0720.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_nbd_refined0.2050.2593
X-RAY DIFFRACTIONr_nbd_other0.1870.22189
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21416
X-RAY DIFFRACTIONr_nbtor_other0.0810.21526
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.195102163
X-RAY DIFFRACTIONr_mcbond_other1.10310663
X-RAY DIFFRACTIONr_mcangle_it4.798162709
X-RAY DIFFRACTIONr_scbond_it4.712101513
X-RAY DIFFRACTIONr_scangle_it6.516161260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.605→1.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 140 -
Rwork0.311 2648 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2388-2.11691.30751.0736-0.49541.91670.0979-0.1787-0.3131-0.10760.08360.22570.0192-0.4342-0.1815-0.0741-0.0408-0.01570.09320.08690.0784-22.3196.24246.007
20.82070.13120.03140.85640.03561.21670.01940.01360.0027-0.14530.0080.047-0.05650.0278-0.0274-0.07980.0129-0.0019-0.10070.0092-0.09213.779.23342.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 11618 - 115
2X-RAY DIFFRACTION2AA2 - 181 - 17
3X-RAY DIFFRACTION2AA117 - 329116 - 328

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