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- PDB-6pxo: Human Casein Kinase 1 delta (anion-free crystallization conditions) -

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Basic information

Entry
Database: PDB / ID: 6pxo
TitleHuman Casein Kinase 1 delta (anion-free crystallization conditions)
ComponentsCasein kinase I isoform delta
KeywordsCIRCADIAN CLOCK PROTEIN / Kinase / serine-threonine kinase
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 / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / 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 / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 ...: / 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 Å
AuthorsFreeberg, A. / 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


Theoretical massNumber of molelcules
Total (without water)68,4132
Polymers68,4132
Non-polymers00
Water5,134285
1
A: Casein kinase I isoform delta


Theoretical massNumber of molelcules
Total (without water)34,2071
Polymers34,2071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta


Theoretical massNumber of molelcules
Total (without water)34,2071
Polymers34,2071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-13 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.910, 130.490, 51.160
Angle α, β, γ (deg.)90.00, 112.75, 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: 34206.531 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.15 M Succinic Acid 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2→65.24 Å / Num. obs: 40494 / % possible obs: 99.6 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.045 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5884 / CC1/2: 0.61 / Rpim(I) all: 0.468 / % possible all: 99.7

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Processing

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

5x17


Resolution: 2→65.24 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2375 1994 4.93 %
Rwork0.1791 --
obs0.1819 40456 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→65.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 0 285 4984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084841
X-RAY DIFFRACTIONf_angle_d0.9656522
X-RAY DIFFRACTIONf_dihedral_angle_d5.3143441
X-RAY DIFFRACTIONf_chiral_restr0.054683
X-RAY DIFFRACTIONf_plane_restr0.006836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05010.32411720.26752690X-RAY DIFFRACTION100
2.0501-2.10550.30081330.25682756X-RAY DIFFRACTION100
2.1055-2.16740.33381490.24372746X-RAY DIFFRACTION99
2.1674-2.23740.28661500.22732730X-RAY DIFFRACTION100
2.2374-2.31740.31691270.21872758X-RAY DIFFRACTION100
2.3174-2.41020.31711700.21072710X-RAY DIFFRACTION100
2.4102-2.51990.27051120.20972786X-RAY DIFFRACTION100
2.5199-2.65270.26131440.19782749X-RAY DIFFRACTION100
2.6527-2.81890.27021260.19112765X-RAY DIFFRACTION100
2.8189-3.03660.20921380.17972736X-RAY DIFFRACTION100
3.0366-3.34210.23361670.17532740X-RAY DIFFRACTION99
3.3421-3.82570.21611430.15492746X-RAY DIFFRACTION99
3.8257-4.81980.18611360.1352741X-RAY DIFFRACTION99
4.8198-65.27970.20251270.16542809X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.88542.8086-1.39145.35960.22432.4685-0.29480.23330.1008-0.62890.05750.2013-0.174-0.16370.20160.2553-0.02-0.12980.30070.01220.3698-22.1364-31.9446-20.4648
23.09530.3416-1.0472.60940.23352.3008-0.03530.12540.1715-0.1063-0.01050.5652-0.1114-0.25430.04030.223-0.0223-0.03810.1842-0.00580.2559-12.0948-18.6688-10.7759
32.75420.4628-0.59082.66191.00712.42950.0317-0.3793-0.13390.2992-0.10670.32830.1330.13510.02250.2258-0.02760.02480.21480.02940.1909-6.3966-18.06260.6429
44.3622-1.5221.0715.16321.17274.2782-0.07260.42810.2705-0.4915-0.0058-0.0133-0.40620.25290.03220.2294-0.0730.01850.26070.02220.290.5248-33.9348-24.0921
55.25263.15372.16736.53742.45092.64960.00030.42360.252-0.56730.0966-0.3755-0.21550.0636-0.1310.18880.01690.06970.31360.00590.20497.3187-44.3871-22.9926
63.4085-0.60240.16534.1494-0.34061.2105-0.03420.10450.05490.01710.14170.59840.0386-0.0234-0.07160.1867-0.0172-0.00570.185-0.00820.2327-3.8931-57.5407-19.1222
74.7918-0.6429-0.30221.6193-1.30092.9038-0.1604-0.4306-0.04540.50450.30730.9399-0.1081-0.1946-0.07280.27650.0240.0980.2340.06150.425-10.9175-59.6923-9.0872
83.3831-0.8235-0.66551.78050.19142.6231-0.2354-0.1827-0.7890.22690.26391.20770.3716-0.13580.07280.3481-0.00260.05820.2430.0980.6832-10.6532-68.6783-13.805
91.30792.5385-0.79588.60931.13722.4497-0.06230.713-0.3145-1.16850.88740.64130.6395-0.6958-0.40430.6074-0.2729-0.38170.75440.09891.3206-23.3859-59.0056-29.6074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 167 )
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 292 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 41 )
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 83 )
6X-RAY DIFFRACTION6chain 'B' and (resid 84 through 191 )
7X-RAY DIFFRACTION7chain 'B' and (resid 192 through 222 )
8X-RAY DIFFRACTION8chain 'B' and (resid 223 through 277 )
9X-RAY DIFFRACTION9chain 'B' and (resid 278 through 292 )

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