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- PDB-5xvu: Crystal structure of the protein kinase CK2 catalytic domain from... -

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Basic information

Entry
Database: PDB / ID: 5xvu
TitleCrystal structure of the protein kinase CK2 catalytic domain from Plasmodium falciparum bound to ATP
ComponentsCasein kinase 2, alpha subunit
KeywordsTRANSFERASE / Casein Kinase 2 Plasmodium falciparum Kinase
Function / homology
Function and homology information


Condensation of Prometaphase Chromosomes / Regulation of TP53 Activity through Phosphorylation / protein kinase CK2 complex / peptidyl-threonine phosphorylation / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein phosphorylation / protein serine/threonine kinase activity ...Condensation of Prometaphase Chromosomes / Regulation of TP53 Activity through Phosphorylation / protein kinase CK2 complex / peptidyl-threonine phosphorylation / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein phosphorylation / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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. ...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
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Casein kinase 2, alpha subunit
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsEl Sahili, A. / Lescar, J. / Ruiz-Carrillo, D. / Lin, J.Q.
CitationJournal: Sci Rep / Year: 2018
Title: The protein kinase CK2 catalytic domain from Plasmodium falciparum: crystal structure, tyrosine kinase activity and inhibition.
Authors: Ruiz-Carrillo, D. / Lin, J.Q. / El Sahili, A. / Wei, M. / Sze, S.K. / Cheung, P.C.F. / Doerig, C. / Lescar, J.
History
DepositionJun 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 3, 2021Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase 2, alpha subunit
B: Casein kinase 2, alpha subunit
C: Casein kinase 2, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,57819
Polymers119,1153
Non-polymers2,46316
Water2,612145
1
A: Casein kinase 2, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4686
Polymers39,7051
Non-polymers7635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15960 Å2
MethodPISA
2
B: Casein kinase 2, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5026
Polymers39,7051
Non-polymers7975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16370 Å2
MethodPISA
3
C: Casein kinase 2, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6087
Polymers39,7051
Non-polymers9036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.410, 123.550, 125.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Casein kinase 2, alpha subunit / Casein kinase II / alpha subunit / putative


Mass: 39704.973 Da / Num. of mol.: 3 / Fragment: UNP residues 12-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF11_0096, PF3D7_1108400 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IIR9, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 161 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium Sulfate, 0.1M BIS-TRIS PH5.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 28155 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 70.47 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.198 / Net I/σ(I): 7.82
Reflection shellRmerge(I) obs: 0.821 / CC1/2: 0.614

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSZ

3nsz


Resolution: 3→29.6 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.899 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.349
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1405 5 %RANDOM
Rwork0.172 ---
obs0.174 28101 99.7 %-
Displacement parametersBiso mean: 50.99 Å2
Baniso -1Baniso -2Baniso -3
1-5.3552 Å20 Å20 Å2
2---1.3046 Å20 Å2
3----4.0506 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 3→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8109 0 144 145 8398
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098486HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0711471HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3037SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes207HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1212HARMONIC5
X-RAY DIFFRACTIONt_it8486HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion19.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1058SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9508SEMIHARMONIC4
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.285 143 4.98 %
Rwork0.236 2728 -
all0.238 2871 -
obs--99.14 %
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)
11.75840.91620.2661.5810.09661.21850.0295-0.06280.00280.0513-0.0210.03510.18340.0249-0.0085-0.06910.0169-0.0139-0.0303-0.0088-0.21271.8429-18.3997-7.989
23.1531-1.0733-0.39192.09850.5481.78290.0156-0.03560.4940.0481-0.012-0.1296-0.2467-0.0644-0.0036-0.1573-0.0178-0.0092-0.0940.067-0.1201-27.567912.4404-0.4955
31.71940.0291-0.6720.60680.47262.0601-0.0081-0.0260.236-0.07920.07580.1258-0.1683-0.0525-0.0676-0.08480.0044-0.016-0.0765-0.0007-0.095712.812-3.146532.4726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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