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- PDB-1eh4: BINARY COMPLEX OF CASEIN KINASE-1 FROM S. POMBE WITH AN ATP COMPE... -

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Basic information

Entry
Database: PDB / ID: 1eh4
TitleBINARY COMPLEX OF CASEIN KINASE-1 FROM S. POMBE WITH AN ATP COMPETITIVE INHIBITOR, IC261
ComponentsCASEIN KINASE-1
KeywordsTRANSFERASE / PROTEIN KINASE / CASEIN KINASE-1 / PROTEIN-INHIBITOR BINARY COMPLEX
Function / homology
Function and homology information


fungal-type vacuole / regulation of endocytosis / endocytosis / positive regulation of canonical Wnt signaling pathway / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding ...fungal-type vacuole / regulation of endocytosis / endocytosis / positive regulation of canonical Wnt signaling pathway / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm
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-IC1 / Casein kinase I homolog 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsMashhoon, N. / Demaggio, A.J. / Tereshko, V. / Bergmeier, S.C. / Egli, M. / Hoekstra, M.F. / Kuret, J.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Crystal Structure of a Conformation-Selective Casein Kinase-1 Inhibitor
Authors: Mashhoon, N. / Demaggio, A.J. / Tereshko, V. / Bergmeier, S.C. / Egli, M. / Hoekstra, M.F. / Kuret, J.
#1: Journal: Embo J. / Year: 1995
Title: Crystal Structure of Casein Kinase-1, a Phosphate-directed Protein Kinase
Authors: Xu, R.M. / Carmel, G. / Sweet, R.M. / Kuret, J. / Cheng, X.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Structural Basis for Selectivity of the Isoquinoline Sulfonamide Family of Protein Kinase Inhibitors
Authors: Xu, R.M. / Carmel, G. / Kuret, J. / Cheng, X.
History
DepositionFeb 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CASEIN KINASE-1
B: CASEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,43415
Polymers68,7542
Non-polymers1,67913
Water84747
1
A: CASEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2658
Polymers34,3771
Non-polymers8887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CASEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1697
Polymers34,3771
Non-polymers7926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.500, 113.500, 110.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Detailstwo molecules in the asymmetric unit are related by a 1/2c translation and a 4 degree rotation along crystal b axis

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Components

#1: Protein CASEIN KINASE-1


Mass: 34377.238 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE RESIDUES 1 - 298
Source method: isolated from a genetically manipulated source
Details: A 298 RESIDUE TRUNCATION MUTANT OF CKI1
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Description: SCHIZOSACCHAROMYCES POMBE / Plasmid: PT7B / Production host: Escherichia coli (E. coli)
References: UniProt: P40233, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4 / Details: IC261 was supplied by ICOS
#3: Chemical ChemComp-IC1 / 3-[(2,4,6-TRIMETHOXY-PHENYL)-METHYLENE]-INDOLIN-2-ONE / IC261


Mass: 311.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Ammonium Sulfate, Sodium Acetate, MPD , pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
210 mMMOPS1drop
30.1 mMEGTA1drop
40.1 %2-mercaptoethanol1drop
5100 mM1dropNaCl
62 %(v/v)1dropMe2SO
71.5-1.6 Mammonium sulfate1reservoir
85 mMsodium acetate1reservoir
91 %MPD1reservoir

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 26, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→98 Å / Num. obs: 18625 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: -0.2 Å2 / Rmerge(I) obs: 0.109
Reflection shellResolution: 2.8→2.97 Å / Num. unique all: 2283 / % possible all: 76.4
Reflection
*PLUS
Lowest resolution: 98 Å / Num. measured all: 98304
Reflection shell
*PLUS
% possible obs: 76.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
bioteXdata reduction
bioteXdata scaling
RefinementResolution: 2.8→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1991701.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: standard cns values
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1832 9.8 %RANDOM
Rwork0.224 ---
obs0.224 18625 95.5 %-
all-18625 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.71 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å211.19 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-6 Å
Luzzati sigma a0.69 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 101 47 4918
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it5.561.5
X-RAY DIFFRACTIONc_mcangle_it8.892
X-RAY DIFFRACTIONc_scbond_it7.422
X-RAY DIFFRACTIONc_scangle_it10.452.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 247 9.8 %
Rwork0.328 2283 -
obs--76.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SO4.PARSO4.TOP
X-RAY DIFFRACTION4261_FINAL.PAR261_FINALA.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.374 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.328

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