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- PDB-2chl: Structure of casein kinase 1 gamma 3 -

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Basic information

Entry
Database: PDB / ID: 2chl
TitleStructure of casein kinase 1 gamma 3
ComponentsCASEIN KINASE I ISOFORM GAMMA-3
KeywordsTRANSFERASE / SERINE/THREONINE KINASE / ATP-BINDING / WNT SIGNALING PATHWAY / KINASE / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding ...protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / 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 ...Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / 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-DKI / Casein kinase I isoform gamma-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. ...Bunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Ugochukwu, E. / Weigelt, J. / von Delft, F. / Knapp, S.
CitationJournal: To be Published
Title: Structure of Casein Kinase 1 Gamma 3
Authors: Bunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Ugochukwu, E. / Weigelt, J. / von Delft, F. / Knapp, S.
History
DepositionMar 15, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 22, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 I ISOFORM GAMMA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9357
Polymers41,0291
Non-polymers9066
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.802, 55.802, 219.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CASEIN KINASE I ISOFORM GAMMA-3 / CASEIN KINASE 1 GAMMA 3 / CKI-GAMMA 3


Mass: 41029.051 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y6M4, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-DKI / 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE / CDK 1/2 INHIBITOR


Mass: 425.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2N7O2S2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCASEIN KINASES ARE OPERATIONALLY DEFINED BY THEIR PREFERENTIAL UTILIZATION OF ACIDIC PROTEINS SUCH ...CASEIN KINASES ARE OPERATIONALLY DEFINED BY THEIR PREFERENTIAL UTILIZATION OF ACIDIC PROTEINS SUCH AS CASEINS AS SUBSTRATES

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growDetails: 1.0 M LI2SO4, 0.5 M TMAO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 25, 2006
RadiationMonochromator: OSMIC HR MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→32.51 Å / Num. obs: 29588 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.49
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C47

2c47


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.444 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1490 5 %RANDOM
Rwork0.183 ---
obs0.186 28033 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 53 260 2732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222538
X-RAY DIFFRACTIONr_bond_other_d0.0020.021762
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9993435
X-RAY DIFFRACTIONr_angle_other_deg0.96834251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95923.025119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53215435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.431519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_nbd_refined0.1860.2589
X-RAY DIFFRACTIONr_nbd_other0.2040.22026
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21237
X-RAY DIFFRACTIONr_nbtor_other0.0880.21389
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.91431517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.84352391
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.73481161
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.155111044
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.467 84
Rwork0.326 1781
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8075-0.26031.64092.8906-0.93421.4488-0.05920.4246-0.0589-0.1533-0.0871-0.14160.040.19720.1463-0.069-0.037-0.0060.07410.0093-0.073617.097236.952828.3327
21.63210.519-0.23811.383-0.24111.5307-0.01070.0311-0.1134-0.0739-0.0504-0.0247-0.0222-0.01720.0611-0.1104-0.0112-0.0087-0.0769-0.0083-0.1316-4.095142.545615.8575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 118
2X-RAY DIFFRACTION2A119 - 333

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