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- PDB-1cki: RECOMBINANT CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RE... -

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Basic information

Entry
Database: PDB / ID: 1cki
TitleRECOMBINANT CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317
ComponentsCASEIN KINASE I DELTA
KeywordsPHOSPHOTRANSFERASE / PROTEIN KINASE
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / 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 / Regulation of PLK1 Activity at G2/M Transition / positive regulation of non-canonical Wnt signaling pathway / COPII-mediated vesicle transport ...Major pathway of rRNA processing in the nucleolus and cytosol / 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 / Regulation of PLK1 Activity at G2/M Transition / positive regulation of non-canonical Wnt signaling pathway / COPII-mediated vesicle transport / protein localization to Golgi apparatus / tau-protein kinase / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / Golgi organization / positive regulation of Wnt signaling pathway / spindle assembly / spindle microtubule / circadian regulation of gene expression / cellular response to nerve growth factor stimulus / regulation of circadian rhythm / spindle / Wnt signaling pathway / endocytosis / kinase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / ciliary basal body / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsLongenecker, K.L. / Roach, P.J. / Hurley, T.D.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Three-dimensional structure of mammalian casein kinase I: molecular basis for phosphate recognition.
Authors: Longenecker, K.L. / Roach, P.J. / Hurley, T.D.
#1: Journal: Embo J. / Year: 1995
Title: Crystal Structure of Casein Kinase-1, a Phosphate-Directed Protein Kinase
Authors: Xu, R. / Carmel, G. / Sweet, R.M. / Kuret, J. / Cheng, X.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Molecular Cloning, Expression, and Characterization of a 49-Kilodalton Casein Kinase I Isoform from Rat Testis
Authors: Graves, P.R. / Haas, D.W. / Hagedorn, C.H. / Depaoli-Roach, A.A. / Roach, P.J.
History
DepositionAug 25, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CASEIN KINASE I DELTA
B: CASEIN KINASE I DELTA


Theoretical massNumber of molelcules
Total (without water)73,9912
Polymers73,9912
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.840, 115.470, 60.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CASEIN KINASE I DELTA


Mass: 36995.531 Da / Num. of mol.: 2
Mutation: C-TERMINAL TRUNCATION MUTANT CONTAINING RESIDUES 1 - 317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: T7 RNA POLYMERASE / Cell line: 293 / Gene: T7 / Organ: TESTES / Plasmid: PET-8C / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): 293
References: UniProt: Q06486, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growDetails: MOLECULE: RECOMBINANT CASEIN KINASE I DELTA. CRYSTALS WERE GROWN BY THE SITTING DROP TECHNIQUE, MIXING 3 MICROLITER OF PROTEIN SOLUTION WITH 3 MICROLITER OF RESERVOIR SOLUTION. THE PROTEIN ...Details: MOLECULE: RECOMBINANT CASEIN KINASE I DELTA. CRYSTALS WERE GROWN BY THE SITTING DROP TECHNIQUE, MIXING 3 MICROLITER OF PROTEIN SOLUTION WITH 3 MICROLITER OF RESERVOIR SOLUTION. THE PROTEIN SOLUTION CONSISTED OF 14 MG/ML PROTEIN IN 50 MM TRIS-HCL (PH=7.5), 1 MM EDTA, 5 MM DTT, 0.2 M NACL, 2.5 MM BETA-OCTYL GLUCOSIDE. THE RESERVOIR SOLUTION CONTAINED 15% PEG 3400, 50 MM SODIUM CITRATE, 50 MM DIBASIC POTASSIUM PHOSPHATE, (PH=6.8). ROOM TEMPERATURE.
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114-16 %PEG34001reservoir
250 mMsodium citrate1reservoir
350 mMpotassium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 11, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→78 Å / Num. obs: 28665 / % possible obs: 76 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Num. measured all: 73172 / Rmerge(I) obs: 0.088

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.279 -7 %
Rwork0.193 --
obs0.193 25781 78 %
Displacement parametersBiso mean: 38.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 0 97 4827
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.601
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.169
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.169

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