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- PDB-1j91: Crystal structure of Z. mays CK2 kinase alpha subunit in complex ... -

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Basic information

Entry
Database: PDB / ID: 1j91
TitleCrystal structure of Z. mays CK2 kinase alpha subunit in complex with the ATP-competitive inhibitor 4,5,6,7-tetrabromobenzotriazole
ComponentsCASEIN KINASE II, ALPHA CHAIN
KeywordsTRANSFERASE / CK2 / casein kinase 2 / inhibitors / tetrabromo-benzotriazole
Function / homology
Function and homology information


regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding ...regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / 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
4,5,6,7-TETRABROMOBENZOTRIAZOLE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsBattistutta, R. / De Moliner, E. / Sarno, S. / Zanotti, G. / Pinna, L.A.
CitationJournal: Protein Sci. / Year: 2001
Title: Structural features underlying selective inhibition of protein kinase CK2 by ATP site-directed tetrabromo-2-benzotriazole.
Authors: Battistutta, R. / De Moliner, E. / Sarno, S. / Zanotti, G. / Pinna, L.A.
History
DepositionMay 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: 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: CASEIN KINASE II, ALPHA CHAIN
B: CASEIN KINASE II, ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4524
Polymers78,5822
Non-polymers8692
Water4,089227
1
A: CASEIN KINASE II, ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7262
Polymers39,2911
Non-polymers4351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CASEIN KINASE II, ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7262
Polymers39,2911
Non-polymers4351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.255, 55.943, 60.302
Angle α, β, γ (deg.)89.77, 102.51, 99.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CASEIN KINASE II, ALPHA CHAIN / CK II / CK2-ALPHA


Mass: 39291.164 Da / Num. of mol.: 2
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-TBS / 4,5,6,7-TETRABROMOBENZOTRIAZOLE / TETRABROMO-2-BENZOTRIAZOLE


Mass: 434.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6HBr4N3
#3: 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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 292 K / Details: Battistutta, R., (2000) J.Biol.Chem., 275, 29618.
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 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 6, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.189→20.445 Å / Num. all: 31302 / Num. obs: 27389 / % possible obs: 87.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.5
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 7.2 / % possible all: 82.8
Reflection
*PLUS
Highest resolution: 2.19 Å / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 82.8 % / Num. unique obs: 3783 / Rmerge(I) obs: 0.093

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→19.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 913215 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1300 4.9 %RANDOM
Rwork0.205 ---
all-29954 --
obs-26659 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.34 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--9.28 Å24.63 Å2-7.08 Å2
2--7.66 Å2-12.63 Å2
3---1.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.22→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 26 227 5707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.273
X-RAY DIFFRACTIONc_mcangle_it4.624
X-RAY DIFFRACTIONc_scbond_it4.724
X-RAY DIFFRACTIONc_scangle_it6.225
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.22→2.36 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 238 5.1 %
Rwork0.232 4412 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TBT.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMTBT.TOP
Refinement
*PLUS
Rfactor obs: 0.205 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.301 / Rfactor Rwork: 0.232 / Rfactor obs: 0.232

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