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- PDB-6rcg: Crystal structure of Casein kinase 1 delta (CK1 delta) complexed ... -

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Basic information

Entry
Database: PDB / ID: 6rcg
TitleCrystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / CSNK1D / CK1 delta / CK1d / kinase inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
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 / circadian regulation of gene expression / spindle microtubule / 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 / 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
Chem-K0E / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Roush, W.R. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor
Authors: Chaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Roush, W.R. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0294
Polymers34,4251
Non-polymers6053
Water6,864381
1
A: Casein kinase I isoform delta
hetero molecules

A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0598
Polymers68,8502
Non-polymers1,2096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3010 Å2
ΔGint-2 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.040, 53.550, 72.170
Angle α, β, γ (deg.)90.000, 113.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34424.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-K0E / ~{N}-[[6,7-bis(fluoranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(3-fluorophenyl)-2-morpholin-4-yl-purin-6-amine


Mass: 480.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19F3N8O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.1M succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.4→66.209 Å / Num. obs: 58592 / % possible obs: 96.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rpim(I) all: 0.031 / Rrim(I) all: 0.06 / Rsym value: 0.051 / Net I/av σ(I): 6.4 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.4-1.483.50.4622.486200.870.2860.5460.46297.5
1.48-1.573.60.2753.980540.1670.3230.27596.8
1.57-1.673.30.1625.872510.1020.1930.16292.4
1.67-1.813.70.1168.571640.0690.1360.11698.3
1.81-1.983.70.07712.366820.0460.090.07798.7
1.98-2.213.60.0571758850.0340.0670.05797.2
2.21-2.563.40.04720.250310.0290.0560.04793.5
2.56-3.133.80.04624.745400.0270.0530.04699.3
3.13-4.433.40.04127.133870.0250.0480.04195.8
4.43-29.6313.90.0429.419780.0240.0470.0498.7

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HNF

4hnf


Resolution: 1.4→29.63 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.202 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0621 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.061
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 2972 5.1 %RANDOM
Rwork0.1419 ---
obs0.1442 55619 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.45 Å2 / Biso mean: 23.78 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.31 Å2
2---1.13 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: final / Resolution: 1.4→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 78 381 2868
Biso mean--22.36 35.04 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192607
X-RAY DIFFRACTIONr_bond_other_d0.0010.022469
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9633522
X-RAY DIFFRACTIONr_angle_other_deg0.85235684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25422.903124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2791522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_rigid_bond_restr8.71832521
X-RAY DIFFRACTIONr_sphericity_bonded12.76852456
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 229 -
Rwork0.217 4127 -
all-4356 -
obs--97.21 %

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