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- PDB-1jam: Crystal structure of apo-form of Z. Mays CK2 protein kinase alpha... -

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Basic information

Entry
Database: PDB / ID: 1jam
TitleCrystal structure of apo-form of Z. Mays CK2 protein kinase alpha subunit
ComponentsCASEIN KINASE II, ALPHA CHAIN
KeywordsTRANSFERASE / protein kinase fold
Function / homology
Function and homology information


protein kinase CK2 complex / regulation of cell cycle / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / 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
Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsBattistutta, R. / De Moliner, E. / Sarno, S. / Zanotti, G. / Pinna, L.A.
CitationJournal: Protein Sci. / Year: 2001
Title: Structural features underlying selective inhibition of protein kinase CK2 by ATP site-directed tetrabromo-2-benzotriazole.
Authors: Battistutta, R. / De Moliner, E. / Sarno, S. / Zanotti, G. / Pinna, L.A.
History
DepositionMay 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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, ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)39,2911
Polymers39,2911
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.830, 58.480, 45.070
Angle α, β, γ (deg.)90.00, 102.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CASEIN KINASE II, ALPHA CHAIN / CK II / CK2-ALPHA


Mass: 39291.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: P28523, EC: 2.7.1.37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 200 mM sodium acetate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K
Crystal grow
*PLUS
Temperature: 292 K / Details: Battistutta, R., (2000) J.Biol.Chem., 275, 29618.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlprotein1drop
2167 mM1dropNaCl
38.3 mMTris-HCl1drop
42 mM2-mercaptoethanol1drop
52 mMATP1drop
60.5 mM1dropMgCl2
725 %PEG40001reservoir
8200 mMsodium acetate1reservoir
9100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 10, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.1→18.79 Å / Num. all: 21211 / Num. obs: 20278 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 4.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 1.9 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 94.6 % / Num. unique obs: 2902 / Rmerge(I) obs: 0.301

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→18.79 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1565622.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 894 4.9 %RANDOM
Rwork0.217 ---
all-19057 --
obs-18085 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.02 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso mean: 47.5 Å2
Baniso -1Baniso -2Baniso -3
1--15.61 Å20 Å2-4.12 Å2
2--28.17 Å20 Å2
3----12.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.18→18.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 0 97 2824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it3.113
X-RAY DIFFRACTIONc_mcangle_it4.344
X-RAY DIFFRACTIONc_scbond_it4.474
X-RAY DIFFRACTIONc_scangle_it6.025
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 155 5.2 %
Rwork0.325 2801 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Rfactor obs: 0.217 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.346 / Rfactor Rwork: 0.325 / Rfactor obs: 0.325

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