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- PDB-1pjk: Crystal Structure of a C-terminal deletion mutant of human protei... -

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Basic information

Entry
Database: PDB / ID: 1pjk
TitleCrystal Structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit
ComponentsCasein kinase II, alpha chain
KeywordsTRANSFERASE / eukaryotic protein kinase fold
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / 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 / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsErmakova, I. / Boldyreff, B. / Issinger, O.-G. / Niefind, K.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit
Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.-G. / Niefind, K.
#1: 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. / Ermakova, I. / Issinger, O.-G.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 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
Remark 999sequence The enzyme CK2 was co crystallized with an artificial peptide substrate (RRRADDSDDDDD). ...sequence The enzyme CK2 was co crystallized with an artificial peptide substrate (RRRADDSDDDDD). However, the peptide could not be located in the electron density.

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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)40,4773
Polymers39,9361
Non-polymers5422
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.044, 46.502, 64.262
Angle α, β, γ (deg.)90.00, 112.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39935.547 Da / Num. of mol.: 1 / Fragment: residue 2-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 OR CK2A1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68400, EC: 2.7.1.37
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEGmme 5000, ammonium sulfate, MES, adenylyl imidodiphosphate, magnesium chloride, peptide RRRADDSDDDDD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 %(w/v)PEG5000 MME1reservoir
20.2 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH7.5
42 mM1dropMgCl2
51 mMAMP-PNP1drop
60.62 mMpeptide1drop

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 2002 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→17.3 Å / Num. all: 11207 / Num. obs: 11207 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 41.3 Å2 / Rsym value: 0.118 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.9
Reflection
*PLUS
Rmerge(I) obs: 0.118
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.9 % / Redundancy: 2.3 % / Num. unique obs: 1136 / Rmerge(I) obs: 0.602

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A of PDB ENTRY 1JWH

1jwh


Resolution: 2.5→17.3 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.297 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC/TLS-REFINEMENT / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25737 1100 9.8 %RANDOM
Rwork0.18027 ---
all0.18792 10099 --
obs0.18792 10099 98.51 %-
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: 12.728 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å21.05 Å2
2---1.52 Å20 Å2
3---3.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→17.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 32 98 2923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212906
X-RAY DIFFRACTIONr_bond_other_d0.0020.022563
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9523938
X-RAY DIFFRACTIONr_angle_other_deg0.76935956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023184
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02633
X-RAY DIFFRACTIONr_nbd_refined0.1820.2593
X-RAY DIFFRACTIONr_nbd_other0.2060.22984
X-RAY DIFFRACTIONr_nbtor_other0.0820.21623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4111.51655
X-RAY DIFFRACTIONr_mcangle_it0.76922691
X-RAY DIFFRACTIONr_scbond_it0.93831251
X-RAY DIFFRACTIONr_scangle_it1.6054.51247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 68
Rwork0.22 773
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)
16.26163.06680.35662.28440.41482.0750.13620.209-0.70860.2373-0.0197-0.49880.09560.2449-0.11660.32630.07770.01310.4901-0.05640.180219.961-65.2-46.406
22.16670.0199-0.56171.4582-0.39912.397-0.01410.12340.16850.12010.0722-0.1265-0.18120.016-0.05810.27160.0006-0.00390.3926-0.01120.0022-3.026-58.888-42.563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1141 - 113
2X-RAY DIFFRACTION2AA115 - 332114 - 331
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 17.3 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.12

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