regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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
Mass: 39878.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli) References: UniProt: P68400, non-specific serine/threonine protein kinase
Resolution: 2.2→2.28 Å / Redundancy: 3.47 % / Mean I/σ(I) obs: 3.4 / % possible all: 59.4
-
Processing
Software
Name
Version
Classification
CrystalClear
datacollection
AMoRE
phasing
REFMAC
5.5.0046
refinement
d*TREK
datareduction
d*TREK
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.01 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: THIS DATA WAS FROM A RECYCLED CRYSTAL
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26919
892
5.2 %
RANDOM
Rwork
0.22094
-
-
-
obs
0.22346
16293
91.58 %
-
all
-
17185
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 58.157 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.28 Å2
0 Å2
0 Å2
2-
-
0.63 Å2
0 Å2
3-
-
-
-0.36 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→29.01 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2762
0
34
138
2934
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.02
2874
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1979
X-RAY DIFFRACTION
r_angle_refined_deg
1.592
1.96
3892
X-RAY DIFFRACTION
r_angle_other_deg
0.989
3
4769
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.347
5
326
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.256
23.05
154
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.718
15
501
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.901
15
25
X-RAY DIFFRACTION
r_chiral_restr
0.104
0.2
399
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
3193
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
626
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.356
43
-
Rwork
0.239
756
-
obs
-
-
57.73 %
Refinement TLS params.
Method: refined / Origin x: 16.5464 Å / Origin y: 21.7148 Å / Origin z: 19.3195 Å
11
12
13
21
22
23
31
32
33
T
0.0072 Å2
0.0026 Å2
0.0023 Å2
-
0.0057 Å2
-0.0028 Å2
-
-
0.0202 Å2
L
0.229 °2
-0.0488 °2
-0.1984 °2
-
0.6575 °2
0.1647 °2
-
-
0.6203 °2
S
0.0385 Å °
0.0085 Å °
-0.0008 Å °
0.0001 Å °
-0.0173 Å °
0.0206 Å °
-0.0187 Å °
0.0281 Å °
-0.0211 Å °
+
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