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- PDB-6xx8: Arabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form II -

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Basic information

Entry
Database: PDB / ID: 6xx8
TitleArabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form II
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: 1.8 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
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

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Assembly

Deposited unit
A: Casein kinase II subunit alpha-1
B: Casein kinase II subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)81,0432
Polymers81,0432
Non-polymers00
Water4,792266
1
A: Casein kinase II subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)40,5221
Polymers40,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)40,5221
Polymers40,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.850, 81.170, 83.460
Angle α, β, γ (deg.)90.000, 105.170, 90.000
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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1.93 Å3/Da / Density % sol: 36.28 %
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: 1.78→46.2 Å / Num. obs: 57878 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 38.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 12
Reflection shellResolution: 1.78→1.89 Å / Num. unique obs: 8433 / CC1/2: 0.175

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHASER1.9_1692phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZH

3pzh


Resolution: 1.8→46.18 Å / SU ML: 0.3454 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.2432 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2458 2797 5.02 %
Rwork0.207 52958 -
obs0.209 55755 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5233 0 0 266 5499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585372
X-RAY DIFFRACTIONf_angle_d0.95887302
X-RAY DIFFRACTIONf_chiral_restr0.0445807
X-RAY DIFFRACTIONf_plane_restr0.0037938
X-RAY DIFFRACTIONf_dihedral_angle_d18.34091932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.46581150.41622052X-RAY DIFFRACTION75.74
1.83-1.860.39041380.38872624X-RAY DIFFRACTION96.61
1.86-1.90.37251400.35042645X-RAY DIFFRACTION96.8
1.9-1.930.32421390.32982640X-RAY DIFFRACTION97.58
1.93-1.980.31951390.32262639X-RAY DIFFRACTION97.41
1.98-2.020.32971410.30882677X-RAY DIFFRACTION97.92
2.02-2.070.30141390.29952630X-RAY DIFFRACTION97.02
2.07-2.130.31381420.27662704X-RAY DIFFRACTION98.82
2.13-2.190.29321400.26452657X-RAY DIFFRACTION97.15
2.19-2.260.30511400.25592658X-RAY DIFFRACTION98.49
2.26-2.340.29181410.23992693X-RAY DIFFRACTION98.57
2.34-2.440.27211400.2282661X-RAY DIFFRACTION97.9
2.44-2.550.27781420.21712678X-RAY DIFFRACTION98.12
2.55-2.680.26911410.21782698X-RAY DIFFRACTION98.61
2.68-2.850.26031420.21912697X-RAY DIFFRACTION98.78
2.85-3.070.28811420.21732684X-RAY DIFFRACTION98.98
3.07-3.380.22871440.20552730X-RAY DIFFRACTION99.17
3.38-3.870.22561420.17052701X-RAY DIFFRACTION98.92
3.87-4.870.17941450.1512751X-RAY DIFFRACTION99.28
4.87-46.180.20511450.17442739X-RAY DIFFRACTION97.63

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