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- PDB-6xx7: Arabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal in com... -

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Basic information

Entry
Database: PDB / ID: 6xx7
TitleArabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal in complex with ANP
ComponentsCasein kinase II subunit alpha-1Casein kinase 2
KeywordsCELL CYCLE / Kinase / CK2 / Casein Kinase
Function / homology
Function and homology information


protein kinase CK2 complex / regulation of circadian rhythm / kinase activity / regulation of cell cycle / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / ATP binding ...protein kinase CK2 complex / regulation of circadian rhythm / kinase activity / regulation of cell cycle / non-specific serine/threonine protein kinase / phosphorylation / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / TRIETHYLENE GLYCOL / Casein kinase II subunit alpha-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

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Assembly

Deposited unit
A: Casein kinase II subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4058
Polymers40,5221
Non-polymers8837
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-53 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.560, 60.560, 228.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Casein kinase 2 / 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 , 6 types, 67 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.44 %
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: 2.4→50 Å / Num. obs: 17625 / % possible obs: 99.6 % / Redundancy: 16.6 % / Biso Wilson estimate: 47.83 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.54 Å / Num. unique obs: 2711 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
PHASER1.14_3260phasing
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZH

3pzh


Resolution: 2.4→47.41 Å / SU ML: 0.3548 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.5707
RfactorNum. reflection% reflection
Rfree0.2464 1593 5.01 %
Rwork0.1954 --
obs0.1979 16027 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 45 60 2733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252760
X-RAY DIFFRACTIONf_angle_d0.54053754
X-RAY DIFFRACTIONf_chiral_restr0.0416406
X-RAY DIFFRACTIONf_plane_restr0.0032476
X-RAY DIFFRACTIONf_dihedral_angle_d17.41421007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.36721340.342595X-RAY DIFFRACTION94.95
2.47-2.560.35531450.30722775X-RAY DIFFRACTION100
2.56-2.660.30991480.2842778X-RAY DIFFRACTION99.97
2.66-2.780.33211440.26982742X-RAY DIFFRACTION100
2.78-2.930.3231430.25752752X-RAY DIFFRACTION100
2.93-3.110.28391370.23292769X-RAY DIFFRACTION99.93
3.11-3.350.26151450.20692791X-RAY DIFFRACTION99.97
3.35-3.690.23881460.1722755X-RAY DIFFRACTION100
3.69-4.230.22731500.14182752X-RAY DIFFRACTION99.93
4.23-5.320.17761510.14042755X-RAY DIFFRACTION100
5.32-47.410.2191500.18922764X-RAY DIFFRACTION99.93

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