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- PDB-2csn: BINARY COMPLEX OF CASEIN KINASE-1 WITH CKI7 -

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Basic information

Entry
Database: PDB / ID: 2csn
TitleBINARY COMPLEX OF CASEIN KINASE-1 WITH CKI7
ComponentsCASEIN KINASE-1
KeywordsPROTEIN KINASE / CASEIN KINASE-1
Function / homology
Function and homology information


fungal-type vacuole / regulation of endocytosis / endocytosis / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / ATP binding ...fungal-type vacuole / regulation of endocytosis / endocytosis / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / ATP binding / nucleus / 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 ...: / 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-CKI / Casein kinase I homolog 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsXu, R.-M. / Cheng, X.
Citation
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.
#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. / Chen, X.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Expression, Purification, Crystallization, and Preliminary X-Ray Analysis of Casein Kinase-1 from Schizosaccharomyces Pombe
Authors: Carmel, G. / Leichus, B. / Cheng, X. / Patterson, S.D. / Mirza, U. / Chait, B.T. / Kuret, J.
History
DepositionOct 11, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CASEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7244
Polymers34,2461
Non-polymers4783
Water2,828157
1
A: CASEIN KINASE-1
hetero molecules

A: CASEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4488
Polymers68,4922
Non-polymers9566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)79.100, 79.100, 120.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CASEIN KINASE-1


Mass: 34246.043 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE RESIDUES 2 - 298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CKI / N-(2-AMINOETHYL)-5-CHLOROISOQUINOLINE-8-SULFONAMIDE


Mass: 285.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12ClN3O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %methanol1reservoir
21.4-1.7 Mammonium sulfate1reservoir
32.5-25 mMsodium acetate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 18581 / % possible obs: 93.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 9999 Å / Observed criterion σ(I): 0 / Num. measured all: 94790 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
HKL(DENZO)data reduction
X-PLORphasing
RefinementResolution: 2.5→31 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.178 --
obs0.178 16391 87.4 %
Refinement stepCycle: LAST / Resolution: 2.5→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 28 157 2571
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.48
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
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_deg23.48
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.61 Å / Total num. of bins used: 8 / Rfactor obs: 0.22

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