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- PDB-1f0q: CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF PROTEIN KINASE CK2 IN C... -

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Basic information

Entry
Database: PDB / ID: 1f0q
TitleCRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF PROTEIN KINASE CK2 IN COMPLEX WITH THE NUCLEOTIDE COMPETITIVE INHIBITOR EMODIN
ComponentsPROTEIN KINASE CK2, ALPHA SUBUNIT
KeywordsTRANSFERASE / protein kinase-inhibitor complex
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 / DNA damage response / 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
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.63 Å
AuthorsBattistutta, R. / Sarno, S. / De Moliner, E. / Papinutto, E. / Zanotti, G. / Pinna, L.A.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: The replacement of ATP by the competitive inhibitor emodin induces conformational modifications in the catalytic site of protein kinase CK2.
Authors: Battistutta, R. / Sarno, S. / De Moliner, E. / Papinutto, E. / Zanotti, G. / Pinna, L.A.
#1: Journal: Embo J. / Year: 1998
Title: Crystal Structure of the Catalitic 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.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: GTP Plus Water Mimic ATP in the Active Site of Protein Kinase CK2
Authors: Niefind, K. / Putter, M. / Guerra, B. / Issinger, O.G. / Schomburg, D.
History
DepositionMay 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PROTEIN KINASE CK2, ALPHA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5612
Polymers39,2911
Non-polymers2701
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.084, 52.080, 44.878
Angle α, β, γ (deg.)90.00, 99.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN KINASE CK2, ALPHA SUBUNIT / CK II


Mass: 39291.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: P28523, EC: 2.7.1.37
#2: Chemical ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, sodium acetate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
pH: 8.5
Details: Guerra, B., (1998) Acta Crystallogr., Sect.D, 54, 143.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlprotein1drop
2167 mM1dropNaCl
38.3 mMTris-HCl1drop
42 mM2-mercaptoethanol1drop
52 mMATP1drop
60.5 mM1dropMgCl2
725 %PEG40001reservoir
8200 mMsodium acetate1reservoir
9100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.63→25.7 Å / Num. all: 8792 / Num. obs: 8792 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.3
Reflection shellResolution: 2.63→2.77 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.156 / % possible all: 83.6
Reflection
*PLUS
Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 83.6 % / Num. unique obs: 1186 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.63→24.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000812.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 932 10.7 %RANDOM
Rwork0.192 ---
obs0.192 8751 89 %-
all-8792 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8316 Å2 / ksol: 0.343965 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å20 Å2-8.08 Å2
2--5.65 Å20 Å2
3----1.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.63→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 20 58 2824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it3.321.5
X-RAY DIFFRACTIONc_mcangle_it5.192
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_scangle_it6.242.5
LS refinement shellResolution: 2.63→2.79 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 148 10.9 %
Rwork0.271 1212 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2EMODIN.PARAMEMODIN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.357 / % reflection Rfree: 10.9 % / Rfactor Rwork: 0.271

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