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- PDB-4jjr: A P21 crystal form of mammalian casein kinase 1 delta -

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Basic information

Entry
Database: PDB / ID: 4jjr
TitleA P21 crystal form of mammalian casein kinase 1 delta
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / CK1D / kinase / casein 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 / protein localization to Golgi apparatus / 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 ...Major pathway of rRNA processing in the nucleolus and cytosol / COPII-mediated vesicle transport / positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / 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 / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / tau-protein kinase activity / Golgi organization / positive regulation of Wnt signaling pathway / spindle assembly / ciliary basal body / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4078 Å
AuthorsZeringo, N.A. / Bellizzi, J.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: A monoclinic crystal form of casein kinase 1 delta
Authors: Zeringo, N.A. / Murphy, L. / McCloskey, E.A. / Rohal, L. / Bellizzi, J.J.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Structure summary
Revision 1.2Aug 21, 2013Group: Data collection / Derived calculations
Revision 1.3Oct 9, 2013Group: Database references
Revision 1.4Oct 16, 2013Group: Database references
Revision 1.5Sep 20, 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)69,4522
Polymers69,4522
Non-polymers00
Water1,56787
1
A: Casein kinase I isoform delta


Theoretical massNumber of molelcules
Total (without water)34,7261
Polymers34,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase I isoform delta


Theoretical massNumber of molelcules
Total (without water)34,7261
Polymers34,7261
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 area3530 Å2
ΔGint-16 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.145, 102.251, 64.593
Angle α, β, γ (deg.)90.000, 101.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34726.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Csnk1d, Hckid / Plasmid: pLIC-HTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9DC28, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 100 mM succinic acid, 15% PEG 3350, pH 7.0, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2012
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 25594 / Num. obs: 25594 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.094 / Χ2: 0.924 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.477.70.68121550.7421100
2.47-2.557.70.55620970.751100
2.55-2.647.70.43121150.7781100
2.64-2.757.70.31921250.7871100
2.75-2.877.70.25721320.8271100
2.87-3.027.70.19621110.881100
3.02-3.217.70.14921560.9671100
3.21-3.467.70.1121171.0921100
3.46-3.817.70.08821271.1091100
3.81-4.367.70.06321351.0751100
4.36-5.497.70.04921341.067199.9
5.49-507.50.04421901.009199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.41 Å40.67 Å
Translation5.24 Å40.67 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.5.0phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UZP CHAIN A

3uzp


Resolution: 2.4078→40.665 Å / Occupancy max: 1 / Occupancy min: 0.55 / FOM work R set: 0.8163 / SU ML: 0.31 / σ(F): 1.35 / Phase error: 25.72 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2371 1279 5 %
Rwork0.2101 24293 -
obs0.2115 25572 99.24 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.27 Å2 / Biso mean: 32.2319 Å2 / Biso min: 10.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4078→40.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 0 87 4727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044744
X-RAY DIFFRACTIONf_angle_d0.9626369
X-RAY DIFFRACTIONf_chiral_restr0.073663
X-RAY DIFFRACTIONf_plane_restr0.003810
X-RAY DIFFRACTIONf_dihedral_angle_d12.941790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4078-2.50420.31191330.27512534266793
2.5042-2.61810.30851430.255227072850100
2.6181-2.75610.28521440.2427222866100
2.7561-2.92870.26581420.246326992841100
2.9287-3.15480.27361420.242126902832100
3.1548-3.47210.27171430.229527302873100
3.4721-3.97420.23471440.209227202864100
3.9742-5.00560.17441420.173827232865100
5.0056-40.67110.21471460.183627682914100

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