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- PDB-1lpu: Low Temperature Crystal Structure of the Apo-form of the catalyti... -

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Basic information

Entry
Database: PDB / ID: 1lpu
TitleLow 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 / 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 / FOURIER SYNTHESIS / Resolution: 1.86 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 8, 2002Deposition site: RCSB / Processing site: PDBJ
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 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
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.190, 59.758, 45.082
Angle α, β, γ (deg.)90.00, 103.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1329-

HOH

21A-1330-

HOH

31A-1331-

HOH

41A-1332-

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 / Production host: Escherichia coli (E. coli) / 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.: 331 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: PEG3350, Tris/HCl, sodium acetate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / 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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 20, 1998 / Details: double mirrors
RadiationMonochromator: Ni-filter + double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→69.6 Å / Num. all: 31554 / Num. obs: 31230 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.084 / Net I/σ(I): 28.4
Reflection shellResolution: 1.86→1.92 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4 / Num. unique all: 2845 / Rsym value: 0.473 / % possible all: 89.8
Reflection
*PLUS
Lowest resolution: 69 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 89.8 % / Rmerge(I) obs: 0.473

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1a6o

1a6o
PDB Unreleased entry


Resolution: 1.86→69.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1572 5 %RANDOM
Rwork0.20421 ---
obs0.20637 29657 99.56 %-
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: 22.307 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å2-1.45 Å2
2--1.25 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.86→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 9 331 3084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212824
X-RAY DIFFRACTIONr_bond_other_d00.022533
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9553826
X-RAY DIFFRACTIONr_angle_other_deg1.26435902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0193334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.59215535
X-RAY DIFFRACTIONr_chiral_restr0.0960.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023119
X-RAY DIFFRACTIONr_gen_planes_other0.010.02595
X-RAY DIFFRACTIONr_nbd_refined0.240.3741
X-RAY DIFFRACTIONr_nbd_other0.2190.32669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.5269
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1240.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.322
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.365
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.517
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0020.51
X-RAY DIFFRACTIONr_mcbond_it0.861.51644
X-RAY DIFFRACTIONr_mcangle_it1.51222672
X-RAY DIFFRACTIONr_scbond_it2.1431180
X-RAY DIFFRACTIONr_scangle_it3.4084.51154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.858→1.906 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 97
Rwork0.256 2039
Refinement
*PLUS
Lowest resolution: 69 Å / Rfactor obs: 0.204 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.204
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_deg1.438

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