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- PDB-3pwd: Crystal structure of maize CK2 in complex with NBC (Z1) -

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Basic information

Entry
Database: PDB / ID: 3pwd
TitleCrystal structure of maize CK2 in complex with NBC (Z1)
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding ...regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / 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
Chem-CZ0 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body / Resolution: 2.2 Å
AuthorsBattistutta, R. / Mazzorana, M.
CitationJournal: Cell.Mol.Life Sci. / Year: 2012
Title: Structural features underlying the selectivity of the kinase inhibitors NBC and dNBC: role of a nitro group that discriminates between CK2 and DYRK1A
Authors: Sarno, S. / Mazzorana, M. / Traynor, R. / Ruzzene, M. / Cozza, G. / Pagano, M.A. / Meggio, F. / Zagotto, G. / Battistutta, R. / Pinna, L.A.
History
DepositionDec 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 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 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5622
Polymers39,2911
Non-polymers2711
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.410, 60.960, 45.660
Angle α, β, γ (deg.)90.000, 100.190, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-338-

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)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CZ0 / 8-hydroxy-4-methyl-9-nitro-2H-benzo[g]chromen-2-one


Mass: 271.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.48 Å3/Da / Density % sol: 50.45 % / Mosaicity: 0.61 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.2M sodium acetate, 0.1M TrisHCl, pH 8, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→70.082 Å / Num. all: 16400 / Num. obs: 16400 / % possible obs: 83.9 % / Redundancy: 2 % / Rsym value: 0.124 / Net I/σ(I): 4.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.321.90.7930.61.1477624910.5120.7930.61.687.4
2.32-2.461.90.5850.4441.3453123330.3770.5850.4442.186.5
2.46-2.6320.5090.3851.7422021610.3290.5090.3852.585.7
2.63-2.8420.3320.2522.6394219880.2130.3320.2523.384.7
2.84-3.1120.2240.174364618200.1440.2240.174.383.9
3.11-3.4820.1430.1096.3330416280.0930.1430.1095.982.5
3.48-4.022.10.0960.0738.6293214280.0610.0960.0737.682.2
4.02-4.922.10.0860.0668.2242211740.0550.0860.0668.780.4
4.92-6.962.10.1020.0777.818719040.0660.1020.0778.478.7
6.96-41.2952.10.1180.0876.39724730.0790.1180.0879.674

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Processing

Software
NameVersionClassificationNB
MOSFLM3.3.16data reduction
SCALA3.3.16data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: Rigid body / Resolution: 2.2→41.295 Å / Occupancy max: 1 / Occupancy min: 0.63 / FOM work R set: 0.8631 / SU ML: 0.34 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 847 5.17 %
Rwork0.1686 --
obs0.1718 16393 83.12 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.873 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 125.68 Å2 / Biso mean: 40.0887 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.1015 Å20 Å21.7229 Å2
2--2.4354 Å20 Å2
3----0.3338 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 20 115 2862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082818
X-RAY DIFFRACTIONf_angle_d1.1253813
X-RAY DIFFRACTIONf_chiral_restr0.082399
X-RAY DIFFRACTIONf_plane_restr0.005487
X-RAY DIFFRACTIONf_dihedral_angle_d13.9231060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.33790.29391370.22132713285087
2.3379-2.51840.28161570.20312624278185
2.5184-2.77170.29591490.21392625277485
2.7717-3.17270.25871220.18442601272383
3.1727-3.99670.21711400.14872531267181
3.9967-41.30240.17771420.13732452259477
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)
10.376-0.39340.1780.3147-0.14090.2234-0.05310.3270.1506-0.0309-0.06230.0441-0.18070.22340.00010.2297-0.159-0.01330.25610.01090.200425.776911.1543-0.0326
20.33920.15710.35650.11290.05860.3935-0.08280.0435-0.01390.0299-0.06420.1166-0.15580.170200.2224-0.0946-0.0110.2038-0.00010.20229.065412.706614.6955
30.38270.35740.07830.3505-0.28080.525-0.0386-0.14060.02070.0326-0.01990.0032-0.150.2206-0.00010.1129-0.01330.00640.1554-0.0110.059815.08742.14412.2622
40.29940.2090.27220.29240.14530.27180.0574-0.003-0.08130.02020.019-0.15960.08010.228600.16210.06390.00280.1521-0.00760.20416.8446-14.53058.951
50.3360.2340.30710.45220.13180.29760.2571-0.1766-0.10550.3152-0.22580.02290.2511-0.02140.00230.19470.1344-0.07230.15920.04710.180313.7624-23.798610.0977
60.06350.099-0.04740.0915-0.03430.0716-0.07480.0587-0.01830.05020.1523-0.07680.0979-0.07100.14350.0145-0.01870.14270.00770.17652.2115-5.5668.5789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:41)A7 - 41
2X-RAY DIFFRACTION2(CHAIN A AND RESID 42:115)A42 - 115
3X-RAY DIFFRACTION3(CHAIN A AND RESID 116:193)A116 - 193
4X-RAY DIFFRACTION4(CHAIN A AND RESID 194:261)A194 - 261
5X-RAY DIFFRACTION5(CHAIN A AND RESID 262:288)A262 - 288
6X-RAY DIFFRACTION6(CHAIN A AND RESID 289:333)A289 - 333

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