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- PDB-3h30: Crystal structure of the catalytic subunit of human protein kinas... -

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Basic information

Entry
Database: PDB / ID: 3h30
TitleCrystal structure of the catalytic subunit of human protein kinase CK2 with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / Protein kinase CK2 / Casein kinase 2 / Casein kinase II / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Wnt signaling pathway
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 / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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
Chem-RFZ / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 Å
AuthorsNiefind, K. / Raaf, J. / Issinger, O.-G.
Citation
Journal: Chem.Biol. / Year: 2008
Title: The CK2alpha/CK2beta Interface of Human Protein Kinase CK2 Harbors a Binding Pocket for Small Molecules
Authors: Raaf, J. / Brunstein, E. / Issinger, O.-G. / Niefind, K.
#1: 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.
#2: 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.
History
DepositionApr 15, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 12, 2009ID: 2RKP
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 alpha
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,11137
Polymers80,0192
Non-polymers2,09235
Water11,115617
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,14417
Polymers40,0101
Non-polymers1,13516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,96720
Polymers40,0101
Non-polymers95719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-369 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.506, 71.506, 125.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II


Mass: 40009.691 Da / Num. of mol.: 2 / Fragment: catalytic subunit, residues 1-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-RFZ / 5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole / 5,6-Dichloro-1-beta-D-ribofuranosylbenzimidazole


Mass: 319.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H12Cl2N2O4
#3: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAS DESCRIBED IN REFERENCE 2 THE GENETIC CONSTRUCT CONTAINS A CODON FOR A FINAL GLYCINE RESIDUE ...AS DESCRIBED IN REFERENCE 2 THE GENETIC CONSTRUCT CONTAINS A CODON FOR A FINAL GLYCINE RESIDUE (GLY335). THIS GLYCINE RESIDUE WAS APPARENTLY LOST DURING PROTEIN PREPARATION OR CRYSTALLIZATION.

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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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5M ammonium sulfate, 0.2M tri-sodium citrate, 0.2M K/Na tartrate pH 5.6, the enzyme was preincubated with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.502
11K,H,-L20.498
ReflectionResolution: 1.56→25 Å / Num. all: 89590 / Num. obs: 89486 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.56→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.474 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.017 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19811 1860 2.1 %RANDOM
Rwork0.15578 ---
all0.15666 89590 --
obs0.15666 87584 99.91 %-
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: 23.844 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---1.02 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.56→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5667 0 92 617 6376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225888
X-RAY DIFFRACTIONr_bond_other_d0.0010.024098
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.967977
X-RAY DIFFRACTIONr_angle_other_deg0.843.0019844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7085674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23523.079315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.674151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6651552
X-RAY DIFFRACTIONr_chiral_restr0.0720.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021282
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.94863360
X-RAY DIFFRACTIONr_mcbond_other0.9261340
X-RAY DIFFRACTIONr_mcangle_it2.49565468
X-RAY DIFFRACTIONr_scbond_it3.21192528
X-RAY DIFFRACTIONr_scangle_it4.0192509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 140 -
Rwork0.174 6457 -
obs--99.94 %
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)
11.2323-0.3436-0.16160.76960.55811.29430.0891-0.07610.16260.0071-0.0002-0.0683-0.1566-0.0791-0.08880.04640.01090.02720.02550.00070.036227.64715.9242.133
20.51680.38-0.76332.1151-0.85191.2887-0.01130.18-0.04760.10330.00110.23380.0961-0.32930.01010.1037-0.05120.00630.1959-0.01270.075513.783-4.529-5.676
30.857-0.4342-0.6451.33820.08030.9970.00480.02640.0759-0.08840.0743-0.19040.0670.1239-0.07910.02810.01250.00080.0676-0.03020.037951.93-8.374-18.704
42.02320.29480.85660.43070.75641.42870.01280.0579-0.27530.2176-0.04870.06940.3979-0.13240.03580.22-0.07510.01370.12930.01140.101331.128-22.237-10.973
520.3684-14.974827.822717.0708-22.874338.9741-1.852-1.0715-0.1151.66381.8696-0.7998-2.4972-1.9356-0.01750.8557-0.5341-0.25411.1243-0.18631.45417.789-2.2988.308
612.978-0.47088.49887.6258-9.637817.00560.33610.2777-0.4452-0.4296-0.4087-0.28650.73330.66450.07250.1284-0.02120.01880.0989-0.00830.130133.416-18.077-23.793
710.7809-6.07920.98669.16535.80027.1466-0.00540.04480.2094-0.0004-0.003-0.10240.02920.0770.00840.301-0.0598-0.03230.3224-0.07210.19996.832-16.5013.038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 12
2X-RAY DIFFRACTION1A117 - 334
3X-RAY DIFFRACTION2A13 - 116
4X-RAY DIFFRACTION3B2 - 12
5X-RAY DIFFRACTION3B117 - 334
6X-RAY DIFFRACTION4B13 - 116
7X-RAY DIFFRACTION5A336
8X-RAY DIFFRACTION6B336
9X-RAY DIFFRACTION7A337

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