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- PDB-1lr4: Room Temperature Crystal Structure of the Apo-form of the catalyt... -

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Basic information

Entry
Database: PDB / ID: 1lr4
TitleRoom Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays
ComponentsProtein kinase CK2
KeywordsTRANSFERASE / protein kinase / CK2 / casein kinase 2 / dual-cosubstrate specificity
Function / homology
Function and homology information


protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity ...protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / cytosol
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
BENZAMIDINE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNiefind, K. / Puetter, M. / Guerra, B. / Issinger, O.-G. / Schomburg, D.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
Authors: Yde, C.W. / Ermakova, I. / Issinger, O.G. / Niefind, K.
#1: Journal: Embo J. / Year: 1998
Title: Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution
Authors: Niefind, K. / Guerra, B. / Pinna, L.A. / Issinger, O.-G. / Schomburg, D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Expression, purification and crystallization of the catalytic subunit of protein kinase CK2 from Zea mays
Authors: Guerra, B. / Niefind, K. / Pinna, L.A. / Schomburg, D. / Issinger, O.-G.
#3: Journal: NAT.STRUCT.BIOL. / Year: 1999
Title: GTP plus water mimic ATP in the active site of protein kinase CK2
Authors: Niefind, K. / Putter, M. / Guerra, B. / Issinger, O.-G. / Schomburg, D.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary characterization of crystals of human protein kinase CK2
Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.-G.
#5: Journal: Embo J. / Year: 2001
Title: Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme
Authors: Niefind, K. / Guerra, B. / Ermakowa, I. / Issinger, O.-G.
#6: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1993
Title: Expression and characterization of a recombinant maize CK-2 alpha subunit
Authors: BOLDYREFF, B. / MEGGIO, F. / DOBROWOLSKA, G. / PINNA, L.A. / Issinger, O.-G.
#7: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1991
Title: Cloning and sequencing of the casein kinase 2 alpha subunit from Zea mays
Authors: DOBROWOLSKA, G. / BOLDYREFF, B. / Issinger, O.-G.
History
DepositionMay 14, 2002Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 29, 2002ID: 1A6O
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase CK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4112
Polymers39,2911
Non-polymers1201
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.550, 61.440, 45.410
Angle α, β, γ (deg.)90.00, 103.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1226-

HOH

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Components

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


Mass: 39291.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pt7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P28523, EC: 2.7.1.37
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG4000, sodium acetate, Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.1 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(w/v)PEG33501reservoir
2200 mMsodium acetate1reservoir
3100 mMTris-HCl1reservoirpH8.1

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 2, 1996 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→26.2 Å / Num. all: 25896 / Num. obs: 24342 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.106
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.7 % / Rsym value: 0.111 / % possible all: 84.9
Reflection
*PLUS
Lowest resolution: 26 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 84.9 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
REFMAC5refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BACKBONE OF CYCLIN-DEPENDENT KINASE 2 (PDB entry 1HCL)

1hcl


Resolution: 2→26 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23675 1247 5.1 %RANDOM
Rwork0.19254 ---
obs0.19487 23092 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.212 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å2-1.32 Å2
2--2.2 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 9 225 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212848
X-RAY DIFFRACTIONr_bond_other_d00.022563
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9553848
X-RAY DIFFRACTIONr_angle_other_deg1.28735983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0693326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.71415552
X-RAY DIFFRACTIONr_chiral_restr0.0990.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023109
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02593
X-RAY DIFFRACTIONr_nbd_refined0.2480.3704
X-RAY DIFFRACTIONr_nbd_other0.2240.32508
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.5216
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1450.510
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4650.515
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1420.51
X-RAY DIFFRACTIONr_mcbond_it0.9261.51641
X-RAY DIFFRACTIONr_mcangle_it1.64922669
X-RAY DIFFRACTIONr_scbond_it2.3431207
X-RAY DIFFRACTIONr_scangle_it3.8054.51179
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 76
Rwork0.216 1523
Refinement
*PLUS
Rfactor obs: 0.193 / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.52
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / Rfactor obs: 0.216

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