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

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Basic information

Entry
Database: PDB / ID: 2oxy
TitleProtein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / inhibitors / tetrabromobenzoimidazole derivatives
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-TETRABROMO-BENZIMIDAZOLE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.812 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4504
Polymers78,5822
Non-polymers8672
Water9,998555
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7252
Polymers39,2911
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7252
Polymers39,2911
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.287, 57.440, 62.467
Angle α, β, γ (deg.)91.90, 103.86, 97.51
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 7 - 333 / Label seq-ID: 2 - 328

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Casein kinase II subunit alpha / 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) / 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-K17 / 4,5,6,7-TETRABROMO-BENZIMIDAZOLE


Mass: 433.720 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H2Br4N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.812→60.52 Å / Num. obs: 55038 / % possible obs: 92 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.1
Reflection shellResolution: 1.812→1.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3.4 / % possible all: 72.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.812→60.52 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.878 / SU B: 3.658 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26856 2775 5 %RANDOM
Rwork0.20729 ---
obs0.21039 52233 93.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.09 Å2-0.1 Å2
2---0.25 Å2-0.11 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.812→60.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 26 555 6035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9647602
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.3195652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69623.862290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.013151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5691538
X-RAY DIFFRACTIONr_chiral_restr0.1350.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024300
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22601
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23756
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0771.53433
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58125286
X-RAY DIFFRACTIONr_scbond_it2.86532668
X-RAY DIFFRACTIONr_scangle_it3.7194.52316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1308tight positional0.160.05
1420loose positional0.675
1308tight thermal0.490.5
1420loose thermal1.6210
LS refinement shellResolution: 1.812→1.859 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 169 -
Rwork0.294 3252 -
obs--78.03 %

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