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- PDB-3c13: Low pH-value crystal structure of emodin in complex with the cata... -

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Basic information

Entry
Database: PDB / ID: 3c13
TitleLow pH-value crystal structure of emodin in complex with the catalytic subunit of protein kinase CK2
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / eukaryotic protein kinases / emodin / ATP-competitive inhibitor / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase / Wnt signaling pathway
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNiefind, K. / Raaf, J. / Issinger, O.-G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Catalytic Subunit of Human Protein Kinase CK2 Structurally Deviates from Its Maize Homologue in Complex with the Nucleotide Competitive Inhibitor Emodin
Authors: Raaf, J. / Klopffleisch, K. / Issinger, O.-G. / Niefind, K.
History
DepositionJan 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4084
Polymers40,0671
Non-polymers3413
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.730, 45.680, 63.240
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40066.742 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: csnk2a1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(de3)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 1.97 Å3/Da / Density % sol: 37.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein stock solution: 10mg/ml protein in 500mM NaCl, 25mM Tris/HCl, pH 8.5 Emodin stock solution: 10mM in water Protein/emodin mixture: equal volumes of protein and emodin stock solutions ...Details: Protein stock solution: 10mg/ml protein in 500mM NaCl, 25mM Tris/HCl, pH 8.5 Emodin stock solution: 10mM in water Protein/emodin mixture: equal volumes of protein and emodin stock solutions were mixed and equillibrated for 30 min prior to crystallization Reservoir: 30% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.6 Crystallization drop: 2 microliters protein/emodin mixture plus 1 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.95→19.7 Å / Num. all: 22799 / Num. obs: 22776 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 13.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2 / Num. unique all: 2247 / Rsym value: 0.626 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BQC

3bqc


Resolution: 1.95→19.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.038 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic plus TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.217 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23346 1161 5.1 %RANDOM
Rwork0.18522 ---
all0.1877 22776 --
obs0.1877 21615 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.78 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å20.37 Å2
2--3.52 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 22 300 3095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222925
X-RAY DIFFRACTIONr_bond_other_d0.0010.022030
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9553971
X-RAY DIFFRACTIONr_angle_other_deg0.91834893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28223.101158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5715513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.861526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
X-RAY DIFFRACTIONr_nbd_refined0.2150.2664
X-RAY DIFFRACTIONr_nbd_other0.1960.22338
X-RAY DIFFRACTIONr_nbtor_refined0.190.21465
X-RAY DIFFRACTIONr_nbtor_other0.0890.21554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.83362172
X-RAY DIFFRACTIONr_mcbond_other1.316666
X-RAY DIFFRACTIONr_mcangle_it4.31592735
X-RAY DIFFRACTIONr_scbond_it3.67461576
X-RAY DIFFRACTIONr_scangle_it4.74891236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.953→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 80 -
Rwork0.222 1554 -
obs--97.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3566-0.0588-0.15161.1635-0.08751.24030.00660.0749-0.00390.13190.0395-0.0405-0.0324-0.008-0.0462-0.14360.0018-0.0065-0.3684-0.0159-0.2803-3.465-58.581-41.836
25.56972.58011.07721.22250.70361.77460.04530.0331-0.50030.17030.0736-0.37420.11280.2454-0.1189-0.12160.047-0.0106-0.179-0.0775-0.098721.469-63.19-46.313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 103 - 10
2X-RAY DIFFRACTION1AA117 - 330117 - 330
3X-RAY DIFFRACTION2AA11 - 11611 - 116

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