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- PDB-6ise: Crystal structure of AMPPNP bound CK2 alpha from C. neoformans -

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Basic information

Entry
Database: PDB / ID: 6ise
TitleCrystal structure of AMPPNP bound CK2 alpha from C. neoformans
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


protein serine/threonine kinase activity / ATP binding
Similarity search - Function
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. ...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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii Bt85 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCho, H.S.
Citation
Journal: To be published
Title: Crystal structure of AMPPNP bound CK2 alpha from C. neoformans
Authors: Cho, H.S.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Evolved to be active: sulfate ions define substrate recognition sites of CK2alpha and emphasise its exceptional role within the CMGC family of eukaryotic protein kinases.
Authors: Niefind, K. / Yde, C.W. / Ermakova, I. / Issinger, O.G.
History
DepositionNov 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
B: Casein kinase II subunit alpha
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6219
Polymers79,1622
Non-polymers1,4597
Water1448
1
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2794
Polymers39,5811
Non-polymers6983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15610 Å2
MethodPISA
2
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3415
Polymers39,5811
Non-polymers7604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.877, 95.594, 93.300
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Casein kinase II subunit alpha / CK2 alpha


Mass: 39580.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii Bt85 (fungus)
Gene: C365_06417
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A226BA59
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000, 30%(w/v) dextran sulfate sodium salt, 2 mM MgCl2, 5 mM AMPPNP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18151 / % possible obs: 97.84 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.7
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.161

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LP4

1lp4


Resolution: 2.8→47.84 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.46 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.364 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22974 928 4.9 %RANDOM
Rwork0.19639 ---
obs0.19808 18151 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.953 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.02 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 86 8 5544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135677
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175175
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.657690
X-RAY DIFFRACTIONr_angle_other_deg1.5721.58411983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2635652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18621.607336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60815988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7471544
X-RAY DIFFRACTIONr_chiral_restr0.0770.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6513.9192614
X-RAY DIFFRACTIONr_mcbond_other2.6483.9182613
X-RAY DIFFRACTIONr_mcangle_it4.4025.8753264
X-RAY DIFFRACTIONr_mcangle_other4.4015.8773265
X-RAY DIFFRACTIONr_scbond_it3.2534.3443062
X-RAY DIFFRACTIONr_scbond_other3.2524.3433063
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2736.3714427
X-RAY DIFFRACTIONr_long_range_B_refined9.31173.80723549
X-RAY DIFFRACTIONr_long_range_B_other9.3173.80623550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.803→2.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 61 -
Rwork0.227 1196 -
obs--87.05 %

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