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- PDB-6xx6: Arabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form I -

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Basic information

Entry
Database: PDB / ID: 6xx6
TitleArabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form I
ComponentsCasein kinase II subunit alpha-1
KeywordsCELL CYCLE / Kinase / CK2 / Casein Kinase / PLANT PROTEIN
Function / homology
Function and homology information


protein kinase CK2 complex / regulation of circadian rhythm / kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / 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
TRIETHYLENE GLYCOL / PIVALIC ACID / Casein kinase II subunit alpha-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84919690899 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9416
Polymers40,5221
Non-polymers4195
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-24 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.98, 61.98, 227.73
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 358 molecules

#2: Chemical ChemComp-PIV / PIVALIC ACID


Type: L-peptide linking / Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
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: 1.849→50 Å / Num. obs: 38648 / % possible obs: 98.7 % / Redundancy: 8.4 % / Biso Wilson estimate: 29.0568885607 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 5815 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASER1.11.1_2575phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZH

3pzh


Resolution: 1.84919690899→48.0095807101 Å / SU ML: 0.245576210565 / Cross valid method: FREE R-VALUE / σ(F): 1.362077121 / Phase error: 20.1312265863
RfactorNum. reflection% reflection
Rfree0.19905896854 3565 5.0086404316 %
Rwork0.173132304507 --
obs0.174441353737 35083 98.2469943545 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.560177005 Å2
Refinement stepCycle: LAST / Resolution: 1.84919690899→48.0095807101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 20 353 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006216939424452894
X-RAY DIFFRACTIONf_angle_d1.065092349813946
X-RAY DIFFRACTIONf_chiral_restr0.0399856326859425
X-RAY DIFFRACTIONf_plane_restr0.00435168801712506
X-RAY DIFFRACTIONf_dihedral_angle_d13.2818014091114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8492-1.87450.4019985125311190.3661497646192252X-RAY DIFFRACTION81.5337001376
1.8745-1.90130.3401986348441310.3264792153432487X-RAY DIFFRACTION91.2831241283
1.9013-1.92970.3171469532741410.3097839717892653X-RAY DIFFRACTION95.717711545
1.9297-1.95980.300038439331380.2868203970892642X-RAY DIFFRACTION96.1272475795
1.9598-1.9920.3123737084971420.2697713869282675X-RAY DIFFRACTION96.6712422787
1.992-2.02630.2673720082331390.2443263517562698X-RAY DIFFRACTION98.4044398196
2.0263-2.06320.2306569475111460.2246780078882728X-RAY DIFFRACTION98.6273164036
2.0632-2.10290.2250556135151450.2020502052262693X-RAY DIFFRACTION99.3349667483
2.1029-2.14580.221096247231470.1929937867362778X-RAY DIFFRACTION99.6592844974
2.1458-2.19240.2475912192471420.1910413576442740X-RAY DIFFRACTION99.8613998614
2.1924-2.24340.2191385175871460.1890879091042735X-RAY DIFFRACTION99.9653018737
2.2434-2.29950.1901469649461530.1740621794072786X-RAY DIFFRACTION99.9319959198
2.2995-2.36170.2271747787991470.1766216448152727X-RAY DIFFRACTION99.8957247132
2.3617-2.43120.2216388062981440.1556802430162764X-RAY DIFFRACTION99.9656239257
2.4312-2.50970.1934237211961500.157512146672748X-RAY DIFFRACTION100
2.5097-2.59940.1880007769831350.1581013270192739X-RAY DIFFRACTION100
2.5994-2.70340.2048206191091460.1720334421392772X-RAY DIFFRACTION100
2.7034-2.82650.1877017955531480.1760272459072763X-RAY DIFFRACTION99.8970487303
2.8265-2.97550.2073935027921440.1780963596462722X-RAY DIFFRACTION100
2.9755-3.16180.2049436099371430.1718936035722754X-RAY DIFFRACTION100
3.1618-3.40590.1612119952361450.1655917134122741X-RAY DIFFRACTION99.9653619674
3.4059-3.74850.1824226628441460.1539869463162763X-RAY DIFFRACTION100
3.7485-4.29070.1690744455761400.1350122210842740X-RAY DIFFRACTION100
4.2907-5.40460.1526509599821430.1335192117772767X-RAY DIFFRACTION99.9656475438
5.4046-48.009580.1923969670021450.1704214506032745X-RAY DIFFRACTION99.4494150034

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