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- PDB-4fi1: Crystal structure of scCK2 alpha in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 4fi1
TitleCrystal structure of scCK2 alpha in complex with ATP
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein-ATP complex / protein kinase / Phosphorylation
Function / homology
Function and homology information


donor selection / Regulation of PTEN stability and activity / Receptor Mediated Mitophagy / Regulation of TP53 Activity through Phosphorylation / Condensation of Prometaphase Chromosomes / regulation of ribosomal protein gene transcription by RNA polymerase II / CURI complex / UTP-C complex / regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III ...donor selection / Regulation of PTEN stability and activity / Receptor Mediated Mitophagy / Regulation of TP53 Activity through Phosphorylation / Condensation of Prometaphase Chromosomes / regulation of ribosomal protein gene transcription by RNA polymerase II / CURI complex / UTP-C complex / regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / nucleolar large rRNA transcription by RNA polymerase I / maturation of SSU-rRNA / small-subunit processome / ribosomal small subunit assembly / regulation of cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / nucleolus / nucleoplasm / 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
ADENOSINE-5'-TRIPHOSPHATE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLiu, H. / Wang, H. / Teng, M. / Li, X.
CitationJournal: To be Published
Title: Crystal structure of scCK2 alpha in complex with ATP
Authors: Liu, H. / Wang, H. / Teng, M. / Li, X.
History
DepositionJun 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,06610
Polymers44,9341
Non-polymers1,1329
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Casein kinase II subunit alpha
hetero molecules

A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,13220
Polymers89,8682
Non-polymers2,26418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area6040 Å2
ΔGint-231 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.773, 69.773, 168.514
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II subunit alpha


Mass: 44933.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CKA1, YIL035C / Production host: Escherichia coli (E. coli)
References: UniProt: P15790, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 4 mM magnesium chloride, 200 mM ammonium sulfate, 100 mM MES (pH 6.2), 20% w/v polyethylene glycol 8000, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9792 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2011
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.09→60.43 Å / Num. obs: 29501
Reflection shellResolution: 2.095→2.149 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→60.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.368 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24317 1452 5.1 %RANDOM
Rwork0.20432 ---
obs0.2063 27225 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å2-0 Å2
2--0.58 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.09→60.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 63 141 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023229
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9654382
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7015374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18323.846156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65615560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7321518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212416
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 78 -
Rwork0.22 1774 -
obs--96.91 %

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