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- PDB-6gro: Human CSNK1G3 bound to SB-223133 -

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Basic information

Entry
Database: PDB / ID: 6gro
TitleHuman CSNK1G3 bound to SB-223133
ComponentsCasein kinase I isoform gamma-3
KeywordsTRANSFERASE / Kinase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein modification process / endocytosis / positive regulation of canonical Wnt signaling pathway / protein kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / 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 ...Casein kinase 1 gamma C-terminal / Casein kinase 1 gamma C terminal / : / 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
Chem-F92 / Casein kinase I isoform gamma-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSzklarz, M. / Vollmar, M. / von Delft, F. / Bountra, C. / Knapp, S. / Edwards, A.M. / Arrowsmith, C. / Elkins, J.M.
CitationJournal: To Be Published
Title: CSNK1G3 bound to SB-223133
Authors: Szklarz, M. / Elkins, J.M.
History
DepositionJun 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Casein kinase I isoform gamma-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1957
Polymers38,5571
Non-polymers6376
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint3 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.750, 56.750, 221.550
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 / CKI-gamma 3


Mass: 38557.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1G3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y6M4, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-F92 / 4-[5-(2-azanylpyrimidin-4-yl)-4-(4-fluorophenyl)imidazol-1-yl]cyclohexan-1-ol


Mass: 353.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20FN5O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium/potassium tartrate, 0.1 M bis-tris-propane pH 8.5, 20% PEG3350, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→49.15 Å / Num. obs: 74333 / % possible obs: 99.6 % / Redundancy: 4.4 % / CC1/2: 0.975 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3637 / CC1/2: 0.617 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZR

2izr


Resolution: 1.45→47.98 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.009 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16732 2979 4 %RANDOM
Rwork0.13367 ---
obs0.13503 71316 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.472 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.45→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 43 365 2773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0142552
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172266
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.6833457
X-RAY DIFFRACTIONr_angle_other_deg1.0661.6545309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9995312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55921.049143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48315439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8371520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0862.2831191
X-RAY DIFFRACTIONr_mcbond_other3.0872.2811190
X-RAY DIFFRACTIONr_mcangle_it3.983.4351492
X-RAY DIFFRACTIONr_mcangle_other3.9833.4381493
X-RAY DIFFRACTIONr_scbond_it3.3912.4671361
X-RAY DIFFRACTIONr_scbond_other3.392.4671362
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2013.6071956
X-RAY DIFFRACTIONr_long_range_B_refined5.69228.5643113
X-RAY DIFFRACTIONr_long_range_B_other5.69128.563114
X-RAY DIFFRACTIONr_rigid_bond_restr2.29134818
X-RAY DIFFRACTIONr_sphericity_free31.0955213
X-RAY DIFFRACTIONr_sphericity_bonded18.29654899
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 245 -
Rwork0.201 5120 -
obs--97.99 %

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