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- PDB-3kxm: Crystal structure of Z. mays CK2 kinase alpha subunit in complex ... -

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Basic information

Entry
Database: PDB / ID: 3kxm
TitleCrystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor K74
ComponentsCasein kinase II subunit alpha
KeywordsTransferase/Transferase inhibitor / Protein kinase CK2-inhibitor complex / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Transferase / Transferase-Transferase inhibitor complex
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
Chem-K74 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body in an isomorphous cell / Resolution: 1.75 Å
AuthorsPapinutto, E. / Franchin, C. / Battistutta, R.
Citation
#1: Journal: Chem.Biol. / Year: 2005
Title: Inspecting the structure-activity relationship of protein kinase CK2 inhibitors derived from tetrabromo-benzimidazole.
Authors: Battistutta, R. / Mazzorana, M. / Sarno, S. / Kazimierczuk, Z. / Zanotti, G. / Pinna, L.A.
#2: Journal: 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
DepositionDec 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2242
Polymers38,6731
Non-polymers5511
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.185, 60.533, 45.873
Angle α, β, γ (deg.)90.000, 103.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 38673.395 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT
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-K74 / N-methyl-2-[(4,5,6,7-tetrabromo-1-methyl-1H-benzimidazol-2-yl)sulfanyl]acetamide


Mass: 550.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9Br4N3OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, 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: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→69.34 Å / Num. obs: 35009 / % possible obs: 91.2 % / Redundancy: 5 % / Biso Wilson estimate: 30.21 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 17.2
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.9 / Num. measured all: 13330 / Num. unique all: 3510 / Rsym value: 0.379 / % possible all: 62.6

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: Rigid body in an isomorphous cell
Resolution: 1.75→69.338 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.064 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1755 5 %RANDOM
Rwork0.224 ---
obs0.227 34991 91.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.01 Å2 / Biso mean: 35.788 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å2-0 Å2-1.23 Å2
2---0.19 Å20 Å2
3---2.67 Å2
Refinement stepCycle: LAST / Resolution: 1.75→69.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 20 179 2920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222810
X-RAY DIFFRACTIONr_angle_refined_deg1.991.9663801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.755325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83823.862145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2715506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8081519
X-RAY DIFFRACTIONr_chiral_restr0.1410.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212149
X-RAY DIFFRACTIONr_mcbond_it1.0961.51626
X-RAY DIFFRACTIONr_mcangle_it1.69322633
X-RAY DIFFRACTIONr_scbond_it2.85331184
X-RAY DIFFRACTIONr_scangle_it4.0644.51168
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 78 -
Rwork0.294 1544 -
all-1622 -
obs--57.29 %
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)
10.82180.55530.19260.48260.17960.3236-0.10040.12820.0211-0.06680.1235-0.1258-0.14970.1968-0.02310.1801-0.0078-00.1846-0.00430.192825.2178.6185-2.8663
21.24430.42440.72950.9220.10091.5352-0.0078-0.07820.03760.05440.0138-0.1348-0.01740.1338-0.00610.1371-0.00020.00890.1260.00990.13928.716812.198814.9009
31.3120.1803-0.01681.2715-0.27311.3543-0.0192-0.09-0.00540.05230.0349-0.09250.06440.1543-0.01580.0914-0.0091-0.02050.09260.00740.107815.7379-1.345510.2832
41.355-0.6955-0.18941.44250.14960.3105-0.0583-0.0018-0.10250.02980.0648-0.12680.16120.1696-0.00650.17890.0053-0.00330.18410.00750.174314.8377-18.060410.5498
50.6303-0.15930.14970.7455-0.3040.2555-0.0536-0.0057-0.1265-0.04130.0423-0.08160.11340.11160.01120.22320.0064-0.01530.2283-0.00170.19879.5782-20.739712.9881
62.8765-0.4535-0.42071.8366-0.36782.2865-0.0164-0.0197-0.00790.02730.00910.0372-0.001-0.04930.00740.0835-0.0283-0.0220.10190.0020.07832.8521-5.55225.9628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 37
2X-RAY DIFFRACTION2A38 - 115
3X-RAY DIFFRACTION3A116 - 220
4X-RAY DIFFRACTION4A221 - 262
5X-RAY DIFFRACTION5A263 - 296
6X-RAY DIFFRACTION6A297 - 332

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