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- PDB-6xx9: Arabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form III -

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Basic information

Entry
Database: PDB / ID: 6xx9
TitleArabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form III
ComponentsCasein kinase II subunit alpha-1
KeywordsCELL CYCLE / Kinase / CK2 / Casein Kinase
Function / homology
Function and homology information


protein kinase CK2 complex / regulation of circadian rhythm / kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / ATP binding / nucleus
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Casein kinase II subunit alpha-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsDemulder, M. / De Veylder, L. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G023616N Belgium
Research Foundation - Flanders (FWO)G011420N Belgium
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of Arabidopsis thaliana casein kinase 2 alpha 1.
Authors: Demulder, M. / De Veylder, L. / Loris, R.
History
DepositionJan 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8364
Polymers40,5221
Non-polymers3143
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-15 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.41, 62.22, 62.08
Angle α, β, γ (deg.)90.0, 106.75, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Casein kinase II subunit alpha-1 / CK II / Casein kinase alpha 1 / AtCKA1


Mass: 40521.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CKA1, At5g67380, K8K14.10 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08467, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium sulfate 0.1M Bis-Tris propane pH 6.5 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.837→50 Å / Num. obs: 33228 / % possible obs: 97.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 35.9412083837 Å2 / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shellResolution: 1.84→1.95 Å / Num. unique obs: 4699 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
PHASER1.9_1692phasing
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZH

3pzh


Resolution: 1.84→42.9819062801 Å / SU ML: 0.279778578395 / Cross valid method: FREE R-VALUE / σ(F): 1.2997274716 / Phase error: 29.9459641375
RfactorNum. reflection% reflection
Rfree0.226809388329 3183 4.98730845163 %
Rwork0.199069494891 --
obs0.200485110195 30045 95.6177805744 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.8045737869 Å2
Refinement stepCycle: LAST / Resolution: 1.84→42.9819062801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 18 180 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005114246334682773
X-RAY DIFFRACTIONf_angle_d0.8046399256283772
X-RAY DIFFRACTIONf_chiral_restr0.0310896412741405
X-RAY DIFFRACTIONf_plane_restr0.00361343391038484
X-RAY DIFFRACTIONf_dihedral_angle_d12.92495912561034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.86470.538133888938730.4758418876641317X-RAY DIFFRACTION47.4726775956
1.8647-1.89380.4201243937921240.4529279375332381X-RAY DIFFRACTION86.4986187845
1.8938-1.92480.3886338881981390.4201172977092597X-RAY DIFFRACTION94.3123061013
1.9248-1.9580.4193829706361380.3889198741062656X-RAY DIFFRACTION96.0797799175
1.958-1.99360.4085741126111390.3472179773162700X-RAY DIFFRACTION97.997928892
1.9936-2.0320.2938231185881390.3062412709872693X-RAY DIFFRACTION98.0609418283
2.032-2.07350.3556875999451410.2834528897042731X-RAY DIFFRACTION98.3561643836
2.0735-2.11850.3056482922021450.2812967949152699X-RAY DIFFRACTION98.75
2.1185-2.16780.288380158021440.2623208557032732X-RAY DIFFRACTION98.8995873453
2.1678-2.2220.3044802695451460.2415993481842779X-RAY DIFFRACTION99.3546195652
2.222-2.28210.2426332251511450.2182659821192704X-RAY DIFFRACTION99.0611961057
2.2821-2.34930.2835745487591370.2241252305532684X-RAY DIFFRACTION98.8437281009
2.3493-2.42510.2238642012851480.1981901504012753X-RAY DIFFRACTION98.4390906006
2.4251-2.51170.2147056877661440.1924758715112717X-RAY DIFFRACTION99.0650969529
2.5117-2.61230.2070393209271400.2054836589362698X-RAY DIFFRACTION98.1667243168
2.6123-2.73120.2192181405971460.2062706192422757X-RAY DIFFRACTION98.8423561457
2.7312-2.87510.2615971103621420.2179109228032701X-RAY DIFFRACTION99.0247300592
2.8751-3.05520.259351211341400.219109357192707X-RAY DIFFRACTION98.9572471324
3.0552-3.2910.2265837056791460.2120803088322773X-RAY DIFFRACTION98.8486285134
3.291-3.62210.192397198211380.1799746116182682X-RAY DIFFRACTION98.0187695516
3.6221-4.14580.2151543395661470.1611525530312738X-RAY DIFFRACTION99.0387916238
4.1458-5.22190.1561363904831420.1398032291652725X-RAY DIFFRACTION99.2728531856
5.2219-42.980.1836433471721400.1549467610862715X-RAY DIFFRACTION98.4143398828
Refinement TLS params.Method: refined / Origin x: 21.1062403897 Å / Origin y: 0.10744297088 Å / Origin z: 12.3993195488 Å
111213212223313233
T0.293418765438 Å2-0.0690939887654 Å20.0103186475887 Å2-0.308633769222 Å2-0.0120345331526 Å2--0.281993312482 Å2
L0.563418512649 °20.188258231642 °20.0978136889198 °2-2.45053378836 °20.00935139613445 °2--1.08693916541 °2
S-0.118910669734 Å °-0.00943689075183 Å °-0.0189084493042 Å °-0.396414334346 Å °0.183255281961 Å °8.92994126718E-5 Å °-0.000339017371922 Å °0.0036061961778 Å °0.00378677178144 Å °
Refinement TLS groupSelection details: Chain A

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