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- PDB-6qs5: Crystal Structure of maize CK2 in complex with tyrphostin AG99 -

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Basic information

Entry
Database: PDB / ID: 6qs5
TitleCrystal Structure of maize CK2 in complex with tyrphostin AG99
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase
Function / homology
Function and homology information


protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / 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-JGB / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.961 Å
AuthorsLolli, G. / Mazzorana, M. / Battistutta, R.
CitationJournal: Biochemistry / Year: 2012
Title: Inhibition of protein kinase CK2 by flavonoids and tyrphostins. A structural insight.
Authors: Lolli, G. / Cozza, G. / Mazzorana, M. / Tibaldi, E. / Cesaro, L. / Donella-Deana, A. / Meggio, F. / Venerando, A. / Franchin, C. / Sarno, S. / Battistutta, R. / Pinna, L.A.
History
DepositionFeb 20, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 27, 2019ID: 4DGO
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,6762
Polymers38,4721
Non-polymers2041
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.970, 59.550, 46.350
Angle α, β, γ (deg.)90.000, 103.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

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Components

#1: Protein Casein kinase II subunit alpha / CK II / CK2-alpha


Mass: 38472.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-JGB / (~{E})-3-[3,4-bis(oxidanyl)phenyl]-2-cyano-prop-2-enamide


Mass: 204.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.49 Å3/Da / Density % sol: 50.61 % / Mosaicity: 0.81 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 0.1 M Tris-HCl, 10-20% PEG 4000, 0.2 M Na-acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.961→69.419 Å / Num. obs: 27064 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Rsym value: 0.07 / Net I/av σ(I): 6.2 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.961-2.073.50.3841.939280.2430.4560.38499.5
2.07-2.193.60.244337680.1510.2880.24499.5
2.19-2.343.60.1913.734890.1170.2240.19199.5
2.34-2.533.60.1255.532500.0770.1480.12599.4
2.53-2.773.60.1036.330130.0630.1210.10399.5
2.77-3.13.60.0748.527430.0450.0870.07499.4
3.1-3.583.50.05110.723990.0320.060.05199.6
3.58-4.383.40.0579.720470.0370.0680.05799.9
4.38-6.23.10.05410.315920.0360.0650.05499
6.2-45.013.40.03315.38350.0220.040.03392.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PVG

3pvg


Resolution: 1.961→34.221 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.38
RfactorNum. reflection% reflection
Rfree0.2189 1352 5.02 %
Rwork0.1846 --
obs0.1863 26929 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.6 Å2 / Biso mean: 51.0985 Å2 / Biso min: 20.97 Å2
Refinement stepCycle: final / Resolution: 1.961→34.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 15 115 2844
Biso mean--36.64 48.71 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062817
X-RAY DIFFRACTIONf_angle_d0.8263813
X-RAY DIFFRACTIONf_chiral_restr0.05401
X-RAY DIFFRACTIONf_plane_restr0.004490
X-RAY DIFFRACTIONf_dihedral_angle_d6.1392374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.961-2.03110.38791400.29992559269999
2.0311-2.11240.3271520.25912528268099
2.1124-2.20850.28341280.22552565269399
2.2085-2.32490.33851030.27382526262997
2.3249-2.47060.27131370.20092548268599
2.4706-2.66120.28861280.2132575270399
2.6612-2.92890.23461420.21122540268299
2.9289-3.35240.21231400.19092583272399
3.3524-4.22250.16121380.1525972735100
4.2225-34.22630.17511440.14232556270096
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)
13.0111.4621.29661.8586-0.1122.3821-0.09040.10290.06410.11530.0072-0.2714-0.52740.3480.0380.3555-0.0122-0.02620.2907-0.05490.333121.79577.926211.3907
22.71420.43210.0292.6922-0.74732.66640.0731-0.0153-0.61220.10850.148-0.68050.47420.4416-0.18080.38410.0944-0.09580.3281-0.11250.512717.4923-13.57619.4129
32.7054-1.25491.01854.6678-1.12713.5182-0.0707-0.0844-0.88180.0280.2865-0.15040.94170.369-0.23040.51390.0091-0.15610.3875-0.0770.63711.1187-21.437610.1876
45.2924-0.58870.48314.2225-1.54244.77070.0104-0.0397-0.27970.11280.28970.04530.243-0.3515-0.25920.2048-0.0042-0.03420.2749-0.01560.22442.4547-6.0416.3706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 184 )A7 - 184
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 256 )A185 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 294 )A257 - 294
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 331 )A295 - 331

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