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- PDB-3ofm: Structure of a human CK2alpha prime, the paralog isoform of the c... -

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Basic information

Entry
Database: PDB / ID: 3ofm
TitleStructure of a human CK2alpha prime, the paralog isoform of the catalytic subunit of protein kinase CK2 from Homo sapiens
ComponentsCasein kinase II subunit alpha'
Keywordstransferase/transferase inhibitor / eukaryptic protein kinase fold / phospho transferase / ATP binding / Phosphorylation / Cytoplasm and nucleus / transferase-transferase inhibitor complex
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / 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 ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / 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 apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / liver regeneration / acrosomal vesicle / Signal transduction by L1 / cerebral cortex development / Regulation of PTEN stability and activity / Wnt signaling pathway / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin / nucleoplasm / ATP 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
Chem-4B0 / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBischoff, N. / Olsen, B. / Raaf, J. / Bretner, M. / Issinger, O.-G. / Niefind, K.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Structural basis of the reduced affinity between the protein kinase CK2 subunits CK2alpha prime and CK2beta
Authors: Bischoff, N. / Olsen, B. / Raaf, J. / Bretner, M. / Issinger, O.G. / Niefind, K.
#1: 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. / Ermakowa, I. / Issinger, O.-G.
#2: Journal: Embo J. / Year: 1998
Title: Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution
Authors: Niefind, K. / Guerra, B. / Pinna, L.A. / Issinger, O.-G. / Schomburg, D.
#3: Journal: CELL.MOL.LIFE SCI. / Year: 2009
Title: Protein kinase CK2: from structures to insights
Authors: Niefind, K. / Raaf, J. / Issinger, O.-G.
History
DepositionAug 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7893
Polymers41,2611
Non-polymers5282
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.690, 47.570, 50.570
Angle α, β, γ (deg.)112.40, 89.49, 91.30
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 41261.176 Da / Num. of mol.: 1 / Mutation: C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CK2A2, CSNK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4B0 / 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol


Mass: 492.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7Br4N3O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein stock solution: 6 mg/ml protein, 25 mM Tris/HCl, pH 8.5, 500 mM sodium chloride, 1 mM inhibitor 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol Reservoir: 28 % PEG6000, 500 mM ...Details: Protein stock solution: 6 mg/ml protein, 25 mM Tris/HCl, pH 8.5, 500 mM sodium chloride, 1 mM inhibitor 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol Reservoir: 28 % PEG6000, 500 mM lithium chloride, 100 mM Tris/HCl, pH 8.5 Drop: mixture of 0.5 uL protein solution plus 0.5 uL reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 6, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→33.03 Å / Num. all: 27265 / Num. obs: 23663 / % possible obs: 86.8 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 26.083 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 12.61
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3.4 / % possible all: 47.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PVR

2pvr


Resolution: 2→33.03 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.974 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20721 1184 5 %RANDOM
Rwork0.17197 ---
obs0.17378 22479 86.8 %-
all-27265 --
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: 26.698 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0.2 Å20.34 Å2
2---0.26 Å2-1.11 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 18 227 2994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222859
X-RAY DIFFRACTIONr_bond_other_d0.0010.022004
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.9573863
X-RAY DIFFRACTIONr_angle_other_deg0.77634834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10223.355152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0521523
X-RAY DIFFRACTIONr_chiral_restr0.060.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
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_it1.4661635
X-RAY DIFFRACTIONr_mcbond_other0.5916654
X-RAY DIFFRACTIONr_mcangle_it2.20862652
X-RAY DIFFRACTIONr_scbond_it2.8991224
X-RAY DIFFRACTIONr_scangle_it4.12791211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 48
Rwork0.196 913
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)
15.052-3.5088-0.23344.0564-0.6830.57130.20330.59060.4662-0.1701-0.13130.1494-0.19260.0008-0.07190.1382-0.0273-0.03790.20220.08830.414314.5919.49-5.092
23.11733.2758-2.27064.3218-2.77192.5552-0.18630.12430.0177-0.25640.1444-0.06320.3117-0.0480.04190.10640.0444-0.00320.0377-0.01280.19058.996-17.0533.995
30.9572-0.3525-0.21581.42890.15611.535-0.0601-0.0301-0.08840.14810.02670.01070.2145-0.0630.03340.0429-0.0155-0.02820.01870.02010.13713.181-4.9595.157
41.8819-0.0461-0.61421.09960.07672.3397-0.02020.35730.0351-0.14660.03960.05560.0538-0.2487-0.01930.0205-0.0153-0.02670.07960.02930.1338-7.4255.274-11.855
52.49650.0973-0.37291.34740.60322.36880.00030.02610.16630.0599-0.00850.0326-0.1562-0.12330.00820.0570.0117-0.02310.00110.02940.1815-8.09714.1883.173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 19
2X-RAY DIFFRACTION2A20 - 77
3X-RAY DIFFRACTION3A78 - 192
4X-RAY DIFFRACTION4A193 - 278
5X-RAY DIFFRACTION5A279 - 332

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