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- PDB-6pxp: Human Casein Kinase 1 delta Site 2 mutant (K171E) -

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Basic information

Entry
Database: PDB / ID: 6pxp
TitleHuman Casein Kinase 1 delta Site 2 mutant (K171E)
ComponentsCasein kinase I isoform delta
KeywordsCIRCADIAN CLOCK PROTEIN/TRANSFERASE / Kinase / serine-threonine kinase / CIRCADIAN CLOCK PROTEIN / CIRCADIAN CLOCK PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / tau-protein kinase / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / tau-protein kinase / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / ciliary basal body / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Circadian Clock / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / 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 / Protein kinases ATP-binding region signature. ...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
Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsYee, L. / Philpott, J.M. / Tripathi, S.M. / Partch, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2020
Title: Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch.
Authors: Philpott, J.M. / Narasimamurthy, R. / Ricci, C.G. / Freeberg, A.M. / Hunt, S.R. / Yee, L.E. / Pelofsky, R.S. / Tripathi, S. / Virshup, D.M. / Partch, C.L.
History
DepositionJul 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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

Downloads & links

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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)69,37412
Polymers68,4132
Non-polymers96110
Water2,072115
1
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6876
Polymers34,2061
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6876
Polymers34,2061
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-142 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.060, 130.350, 51.650
Angle α, β, γ (deg.)90.00, 113.47, 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: 34206.465 Da / Num. of mol.: 2 / Fragment: K171E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli (E. coli)
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7.7 mg/mL Protein 0.05 M Sodium Acetate 0.35 M Ammonium Sulfate 17.5% PEG 3500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.35→47.38 Å / Num. obs: 25271 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.077 / Net I/σ(I): 6.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2470 / CC1/2: 0.77 / Rpim(I) all: 0.404

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X17

5x17


Resolution: 2.35→45.918 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 28.35
RfactorNum. reflection% reflection
Rfree0.2433 1253 4.98 %
Rwork0.1985 --
obs0.2009 25175 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→45.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 50 115 4922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094915
X-RAY DIFFRACTIONf_angle_d1.1916610
X-RAY DIFFRACTIONf_dihedral_angle_d8.5812916
X-RAY DIFFRACTIONf_chiral_restr0.061681
X-RAY DIFFRACTIONf_plane_restr0.007837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.44410.3031390.26492649X-RAY DIFFRACTION100
2.4441-2.55530.28951390.25082634X-RAY DIFFRACTION100
2.5553-2.690.32251310.24672653X-RAY DIFFRACTION100
2.69-2.85850.28431110.23592680X-RAY DIFFRACTION100
2.8585-3.07920.27751410.23392662X-RAY DIFFRACTION100
3.0792-3.3890.30541200.22112679X-RAY DIFFRACTION100
3.389-3.87920.27231470.18842641X-RAY DIFFRACTION99
3.8792-4.88650.18441620.14922646X-RAY DIFFRACTION100
4.8865-45.92710.18891630.16652678X-RAY DIFFRACTION100

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