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- PDB-4rlk: Crystal structure of Z. mays CK2alpha in complex with the ATP-com... -

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Basic information

Entry
Database: PDB / ID: 4rlk
TitleCrystal structure of Z. mays CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR 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 / 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
ACETATE ION / Chem-E91 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsGuerra, B. / Rasmussen, T.D.L. / Schnitzler, A. / Jensen, H.H. / Boldyreff, B.S. / Miyata, Y. / Marcussen, N. / Niefind, K. / Issinger, O.G.
CitationJournal: Cancer Lett / Year: 2015
Title: Protein kinase CK2 inhibition is associated with the destabilization of HIF-1 alpha in human cancer cells.
Authors: Guerra, B. / Rasmussen, T.D. / Schnitzler, A. / Jensen, H.H. / Boldyreff, B.S. / Miyata, Y. / Marcussen, N. / Niefind, K. / Issinger, O.G.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0127
Polymers39,2911
Non-polymers7216
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.748, 59.683, 44.884
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-566-

HOH

21A-611-

HOH

31A-639-

HOH

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Components

#1: Protein Casein kinase II subunit alpha / 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) / Gene: ACK2 / Plasmid: pt7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) C+RP
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-E91 / 4-[(E)-(9H-fluoren-9-ylidenehydrazinylidene)methyl]benzoic acid


Mass: 326.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Reservoir: 20 % PEG 4000, 0.2 M sodium acetate, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 11, 2012
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→43.74 Å / Num. obs: 103023 / % possible obs: 99.09 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 16.08 Å2 / Rmerge(I) obs: 0.01738 / Rsym value: 0.02078 / Net I/σ(I): 27.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.24-1.322.760.5132.21162260.51396.7
1.32-1.412.930.2913.72156510.29199.5
1.41-1.523.320.1627.11146500.16299.7
1.52-1.663.380.08413.5134330.08499.7
1.66-1.863.180.04223.8121850.04299.6
1.86-2.153.410.02344.98107660.02399.6
2.15-2.633.420.01768.0190930.01799.3
2.63-3.713.110.01184.4270450.01198.8
3.71-43.743.610.009105.2639760.00999.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
CORRECTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LP4

1lp4


Resolution: 1.24→43.74 Å / SU ML: 0.12 / σ(F): 1.36 / σ(I): 2.01 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 5140 4.99 %RANDOM
Rwork0.1433 ---
obs0.1449 102946 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 51 324 3102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142987
X-RAY DIFFRACTIONf_angle_d1.4694050
X-RAY DIFFRACTIONf_dihedral_angle_d13.251139
X-RAY DIFFRACTIONf_chiral_restr0.098420
X-RAY DIFFRACTIONf_plane_restr0.009525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.2399-1.2540.34821480.34652809280986
1.254-1.26880.30911530.29043315331599
1.2688-1.28430.28471640.27383254325499
1.2843-1.30050.31551620.25453250325099
1.3005-1.31760.24591480.23473268326899
1.3176-1.33570.26041680.22473258325899
1.3357-1.35480.23461680.20553274327499
1.3548-1.3750.22571640.19313207320799
1.375-1.39650.21111860.184332853285100
1.3965-1.41940.20651770.175532513251100
1.4194-1.44380.20291820.16013272327299
1.4438-1.47010.18151720.154332423242100
1.4701-1.49840.18451580.144433123312100
1.4984-1.5290.16941810.134432583258100
1.529-1.56220.15831690.124432763276100
1.5622-1.59850.13981790.116532483248100
1.5985-1.63850.15511780.115932673267100
1.6385-1.68280.16111770.117732923292100
1.6828-1.73230.17071980.118132903290100
1.7323-1.78830.14751740.12053235323599
1.7883-1.85220.16651500.11933083308100
1.8522-1.92630.15941660.125132853285100
1.9263-2.0140.16221660.128432773277100
2.014-2.12020.16441820.12532913291100
2.1202-2.2530.15991830.12633292329299
2.253-2.4270.14791780.13283242324299
2.427-2.67120.17651890.14753286328699
2.6712-3.05760.17131680.14873277327799
3.0576-3.85190.18141780.14023301330199
3.8519-43.76740.17491740.14333384338499

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