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- PDB-2oxx: Protein kinase CK2 in complex with tetrabromobenzoimidazole deriv... -

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Basic information

Entry
Database: PDB / ID: 2oxx
TitleProtein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 / inhibitors / tetrabromobenzoimidazole derivatives
Function / homology
Function and homology information


protein kinase CK2 complex / regulation of cell cycle / non-specific serine/threonine protein kinase / phosphorylation / 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
4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-THIONE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBattistutta, R. / Zanotti, G. / Cendron, L.
CitationJournal: Chembiochem / Year: 2007
Title: The ATP-Binding Site of Protein Kinase CK2 Holds a Positive Electrostatic Area and Conserved Water Molecules.
Authors: Battistutta, R. / Mazzorana, M. / Cendron, L. / Bortolato, A. / Sarno, S. / Kazimierczuk, Z. / Zanotti, G. / Moro, S. / Pinna, L.A.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7572
Polymers39,2911
Non-polymers4661
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.348, 60.524, 45.492
Angle α, β, γ (deg.)90.00, 102.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II / CK2-alpha


Mass: 39291.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-K22 / 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-THIONE


Mass: 465.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H2Br4N2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M TrisHCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9755
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.3→68.84 Å / Num. obs: 13565 / % possible obs: 82.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.7 / % possible all: 85.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→68.84 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.211 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.677 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27005 749 5.4 %RANDOM
Rwork0.21373 ---
obs0.21693 13154 82.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.68 Å2
Baniso -1Baniso -2Baniso -3
1--5.15 Å20 Å2-3.24 Å2
2---0.06 Å20 Å2
3---3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.3→68.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 14 119 2846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9653784
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.065324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4423.819144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96115505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4531519
X-RAY DIFFRACTIONr_chiral_restr0.0840.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022139
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21278
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21891
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5011.51682
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87422627
X-RAY DIFFRACTIONr_scbond_it1.2231326
X-RAY DIFFRACTIONr_scangle_it1.7614.51157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 56 -
Rwork0.274 1022 -
obs--88.36 %

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