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- PDB-3q04: Crystal structure of the apo-form of human CK2 alpha at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 3q04
TitleCrystal structure of the apo-form of human CK2 alpha at pH 8.5
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase / apo-form
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 / KEAP1-NFE2L2 pathway / kinase activity / 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
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBattistutta, R. / Ranchio, A. / Papinutto, E.
CitationJournal: to be published
Title: Structural and functional analysis of the flexible regions of the catalytic alpha-subunit of protein kinase CK2
Authors: Papinutto, E. / Ranchio, A. / Lolli, G. / Pinna, L.A. / Battistutta, R.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6545
Polymers39,3041
Non-polymers3504
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.686, 46.065, 63.675
Angle α, β, γ (deg.)90.000, 111.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39303.820 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 3-330
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.2M lithium sulfate, 0.1M TrisHCl, pH 8.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→59.24 Å / Num. all: 29505 / Num. obs: 29505 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.93.60.4670.3971.51513642630.2450.4670.3975.399.8
1.9-2.013.60.2930.2492.51449640750.1530.2930.2497.899.8
2.01-2.153.50.1840.1563.91341237940.0970.1840.15611.599.9
2.15-2.323.50.1320.1125.51262235730.070.1320.11215.3100
2.32-2.553.50.0930.0797.81157632960.0490.0930.07918.799.9
2.55-2.853.50.0740.06310.21033129580.0390.0740.06322100
2.85-3.293.50.0690.05810922026560.0370.0690.05826.999.9
3.29-4.023.30.0490.04115.1733622070.0260.0490.04131.299.8
4.02-5.693.30.0340.02821.2568517450.0190.0340.0283699.4
5.69-59.243.30.0320.02722.831059380.0180.0320.02736.894.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ProDCdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 1.8→59.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2253 / WRfactor Rwork: 0.1694 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8782 / SU B: 5.693 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1307 / SU Rfree: 0.1311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 1498 5.1 %RANDOM
Rwork0.1617 ---
obs0.1645 29490 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.14 Å2 / Biso mean: 21.505 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20.19 Å2
2--0.52 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→59.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 19 253 3045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222879
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9523898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77423.097155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66215511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3971525
X-RAY DIFFRACTIONr_chiral_restr0.1490.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212214
X-RAY DIFFRACTIONr_mcbond_it1.251.51648
X-RAY DIFFRACTIONr_mcangle_it2.0522683
X-RAY DIFFRACTIONr_scbond_it3.41131231
X-RAY DIFFRACTIONr_scangle_it5.154.51212
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 122 -
Rwork0.231 2042 -
all-2164 -
obs--99.49 %
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)
15.76261.485-4.84020.53-0.6058.1163-0.46110.3844-0.6308-0.03250.1156-0.14050.5518-0.32090.34550.1438-0.01310.08030.0604-0.0510.2184-3.493-30.996-45.694
23.12862.19350.04382.79630.78461.5461-0.00640.1704-0.39680.16980.0184-0.16140.14830.1574-0.0120.05050.02540.00140.1034-0.04520.122121.808-20.545-47.231
33.971.60540.72971.44560.71390.95910.08530.0464-0.1920.112-0.0577-0.13430.0380.0965-0.02760.0164-0.0026-0.00760.0822-0.02770.071422.844-14.543-46.195
42.3026-1.05710.30174.11721.98542.1057-0.0929-0.02150.75910.3255-0.0839-0.0134-0.3706-0.20570.17680.42220.0566-0.02650.293-0.01450.46488.6241.052-46.594
51.3143-0.0202-0.50610.5623-0.00220.6303-0.02650.0706-0.04890.07750.0175-0.0254-0.0241-0.00760.0090.06350.0028-0.02250.0633-0.01670.0679-1.867-14.223-39.938
60.9569-0.0758-0.36571.43910.04181.21620.02860.23510.0284-0.02220.00770.0845-0.0715-0.1994-0.03630.00870.0053-0.0120.12250.01550.0575-10.487-8.684-49.097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 15
2X-RAY DIFFRACTION2A16 - 49
3X-RAY DIFFRACTION3A50 - 113
4X-RAY DIFFRACTION4A114 - 127
5X-RAY DIFFRACTION5A128 - 280
6X-RAY DIFFRACTION6A281 - 330

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