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- PDB-1m2q: Crystal structure of 1,8-di-hydroxy-4-nitro-xanten-9-one/CK2 kina... -

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Basic information

Entry
Database: PDB / ID: 1m2q
TitleCrystal structure of 1,8-di-hydroxy-4-nitro-xanten-9-one/CK2 kinase complex
ComponentsCasein kinase II, alpha chain
KeywordsTRANSFERASE / kinase / inhibitor-enzyme complex
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 / 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
1,8-DI-HYDROXY-4-NITRO-XANTHEN-9-ONE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsDe Moliner, E. / Sarno, S. / Moro, S. / Zagotto, G. / Zanotti, G. / Pinna, L.A. / Battistutta, R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Inhibition of protein kinase CK2 by anthraquinone-related compounds. A structural insight
Authors: De Moliner, E. / Moro, S. / Sarno, S. / Zagotto, G. / Zanotti, G. / Pinna, L.A. / Battistutta, R.
History
DepositionJun 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Casein kinase II, alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9472
Polymers38,6731
Non-polymers2731
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.040, 51.730, 44.700
Angle α, β, γ (deg.)90.00, 99.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Casein kinase II, alpha chain / CKII


Mass: 38673.395 Da / Num. of mol.: 1 / Fragment: Catlytic subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / 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-MNX / 1,8-DI-HYDROXY-4-NITRO-XANTHEN-9-ONE


Mass: 273.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H7NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.082 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, Sodium Acetate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
210-20 %PEG40001drop
30.2 Msodium acetate1drop
40.1 MTris1droppH8.0
520 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 14, 2002
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→48.57 Å / Num. all: 28179 / Num. obs: 28179 / % possible obs: 79.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.083 / Net I/σ(I): 4.63
Reflection shellResolution: 1.79→1.9 Å / Num. unique all: 2331 / % possible all: 50.1
Reflection
*PLUS
Highest resolution: 1.79 Å / Num. obs: 26331 / % possible obs: 87.6 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Lowest resolution: 1.9 Å / % possible obs: 50.2 % / Redundancy: 3.5 % / Num. unique obs: 2204 / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→29.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 1474647.4 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2110 7.9 %RANDOM
Rwork0.198 ---
all0.2006 30579 --
obs0.198 26543 86.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8254 Å2 / ksol: 0.381165 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-3.43 Å2
2--0.64 Å20 Å2
3----0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.79→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 20 161 2909
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it2.592
X-RAY DIFFRACTIONc_scangle_it4.042.5
LS refinement shellResolution: 1.79→1.9 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 189 7.5 %
Rwork0.251 2331 -
obs-2331 50.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MNX.PARAMMNX.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Rfactor Rfree: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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