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- PDB-1day: CRYSTAL STRUCTURE OF A BINARY COMPLEX OF PROTEIN KINASE CK2 (ALPH... -

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Basic information

Entry
Database: PDB / ID: 1day
TitleCRYSTAL STRUCTURE OF A BINARY COMPLEX OF PROTEIN KINASE CK2 (ALPHA-SUBUNIT) AND MG-GMPPNP
ComponentsPROTEIN KINASE CK2
KeywordsTRANSFERASE / PROTEIN KINASE CK2 / DUAL-COSUBSTRATE SPECIFICITY / BINARY COMPLEX WITH MG-GMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsNiefind, K. / Puetter, M. / Guerra, B. / Issinger, O.G. / Schomburg, D.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: GTP plus water mimic ATP in the active site of protein kinase CK2.
Authors: Niefind, K. / Putter, M. / Guerra, B. / Issinger, O.G. / Schomburg, D.
#1: Journal: Embo J. / Year: 1998
Title: Crystal Structure of the Catalytic Subunit of Protein Kinase CK2 from Zea mays at 2.1 A Resolution
Authors: Niefind, K. / Guerra, B. / Pinna, L.A. / Issinger, O.G. / Schomburg, D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Expression, Purification and Crystallization of the Catalytic Subunit of Protein Kinase CK2 From Zea mays
Authors: Guerra, B. / Niefind, K. / Pinna, L.A. / Schomburg, D. / Issinger, O.G.
#3: Journal: Biochim.Biophys.Acta / Year: 1991
Title: Cloning and Sequencing of the Casein Kinase 2 Alpha Subunit From Zea mays
Authors: Dobrowolska, G. / Boldyreff, B. / Issinger, O.G.
History
DepositionNov 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PROTEIN KINASE CK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2444
Polymers38,6731
Non-polymers5713
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.700, 58.820, 46.180
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

#1: Protein PROTEIN KINASE CK2


Mass: 38673.395 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: P28523, EC: 2.7.1.37
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 3350, SODIUM ACETATE, TRIS/HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 292 K / pH: 8.5
Details: Guerra, B., (1998) Acta Crystallogr., Sect.D, 54, 143.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
2500 mM1dropNaCl
325 mMTris-HCl1drop
47 mM2-mercaptoethanol1drop
56 mMATP1reservoir
61.5 mM1reservoirMgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength
ROTATING ANODEENRAF-NONIUS FR57111.5418
ROTATING ANODEENRAF-NONIUS FR57121.5418
Detector
TypeIDDetectorDate
MAC Science DIP-20301IMAGE PLATENov 10, 1998
MAC Science DIP-20302IMAGE PLATEDec 14, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→54.1 Å / Num. all: 19027 / Num. obs: 19002 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.407 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
RefinementStarting model: 1DAW

1daw


Resolution: 2.2→54.1 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: REFMAC DEFAULT VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.29 981 -RANDOM
Rwork0.212 ---
all0.223 19027 --
obs0.223 19002 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.2→54.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 34 231 2998
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / Rfactor obs: 0.212 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_deg2.8

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