- PDB-4fi1: Crystal structure of scCK2 alpha in complex with ATP -
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Basic information
Entry
Database: PDB / ID: 4fi1
Title
Crystal structure of scCK2 alpha in complex with ATP
Components
Casein kinase II subunit alpha
Keywords
TRANSFERASE / protein-ATP complex / protein kinase / Phosphorylation
Function / homology
Function and homology information
donor selection / 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 ...donor selection / 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 / Regulation of PTEN stability and activity / nucleolar large rRNA transcription by RNA polymerase I / maturation of SSU-rRNA / small-subunit processome / ribosomal small subunit assembly / non-specific serine/threonine protein kinase / regulation of cell cycle / 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
Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2011
Radiation
Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9792 Å / Relative weight: 1
Reflection
Resolution: 2.09→60.43 Å / Num. obs: 29501
Reflection shell
Resolution: 2.095→2.149 Å / % possible all: 100
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
REFMAC
5.6.0117
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24317
1452
5.1 %
RANDOM
Rwork
0.20432
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-
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obs
0.2063
27225
99.61 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 25.464 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.58 Å2
0.29 Å2
-0 Å2
2-
-
0.58 Å2
-0 Å2
3-
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-0.87 Å2
Refinement step
Cycle: LAST / Resolution: 2.09→60.43 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3070
0
63
141
3274
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.02
3229
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.188
1.965
4382
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.701
5
374
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.183
23.846
156
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.656
15
560
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.732
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
468
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2416
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.095→2.149 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.312
78
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Rwork
0.22
1774
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obs
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96.91 %
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