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- PDB-5x17: Crystal structure of murine CK1d in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 5x17
TitleCrystal structure of murine CK1d in complex with ADP
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / CK1D / KINASE
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / COPII-mediated vesicle transport / positive regulation of non-canonical Wnt signaling pathway / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / midbrain dopaminergic neuron differentiation ...Major pathway of rRNA processing in the nucleolus and cytosol / COPII-mediated vesicle transport / positive regulation of non-canonical Wnt signaling pathway / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / midbrain dopaminergic neuron differentiation / Regulation of PLK1 Activity at G2/M Transition / tau-protein kinase / non-motile cilium assembly / tau-protein kinase activity / positive regulation of Wnt signaling pathway / spindle assembly / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / 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 ...: / 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'-DIPHOSPHATE / Casein kinase I isoform delta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKikuchi, M. / Shinohara, Y. / Ueda, H.R. / Umehara, T.
CitationJournal: Mol. Cell / Year: 2017
Title: Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
Authors: Shinohara, Y. / Koyama, Y.M. / Ukai-Tadenuma, M. / Hirokawa, T. / Kikuchi, M. / Yamada, R.G. / Ukai, H. / Fujishima, H. / Umehara, T. / Tainaka, K. / Ueda, H.R.
History
DepositionJan 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase I isoform delta
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,55215
Polymers68,6412
Non-polymers1,91113
Water5,603311
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3248
Polymers34,3211
Non-polymers1,0047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-34 kcal/mol
Surface area13990 Å2
MethodPISA
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2287
Polymers34,3211
Non-polymers9086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.135, 130.349, 53.177
Angle α, β, γ (deg.)90.00, 115.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Casein kinase I isoform delta / CKId / Tau-protein kinase CSNK1D


Mass: 34320.637 Da / Num. of mol.: 2 / Fragment: UNP residues 1-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Csnk1d, Hckid / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q9DC28, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM Na-citrate, 25 mM (NH4)2SO4 and 7 % PEG 8000, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 22, 2016
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 41687 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 15.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2087 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UYS

3uys


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.38 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24155 2039 4.9 %RANDOM
Rwork0.18721 ---
obs0.18996 39503 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.415 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.1 Å2
2---2.57 Å20 Å2
3---1.71 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 0 109 311 5075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194885
X-RAY DIFFRACTIONr_bond_other_d0.0020.024548
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9836603
X-RAY DIFFRACTIONr_angle_other_deg0.966310428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20322.807228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95115840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8521538
X-RAY DIFFRACTIONr_chiral_restr0.0950.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025440
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021204
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_it2.7133.4832321
X-RAY DIFFRACTIONr_mcbond_other2.7123.4822320
X-RAY DIFFRACTIONr_mcangle_it3.9625.2082900
X-RAY DIFFRACTIONr_mcangle_other3.9615.212901
X-RAY DIFFRACTIONr_scbond_it3.1173.7552564
X-RAY DIFFRACTIONr_scbond_other3.1163.7552565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.875.5013703
X-RAY DIFFRACTIONr_long_range_B_refined6.66339.4125660
X-RAY DIFFRACTIONr_long_range_B_other6.66339.4095661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 161 -
Rwork0.266 2910 -
obs--99.9 %

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