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- PDB-2c47: Structure of casein kinase 1 gamma 2 -

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Basic information

Entry
Database: PDB / ID: 2c47
TitleStructure of casein kinase 1 gamma 2
ComponentsCASEIN KINASE 1 GAMMA 2 ISOFORM
KeywordsTRANSFERASE / SERINE/THREONINE KINASE / ACTIN CYTOSKELETON ORGANISATION / ATP-BINDING / WNT SIGNALING PATHWAY
Function / homology
Function and homology information


sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation ...sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine/threonine kinase activity / signal transduction / ATP binding / membrane / nucleus / plasma membrane / cytosol / 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 / Serine/Threonine protein kinases, catalytic 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-5ID / Casein kinase I isoform gamma-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBunkoczi, G. / Rellos, P. / Das, S. / Ugochukwu, E. / Fedorov, O. / Sobott, F. / Eswaran, J. / Amos, A. / Ball, L. / von Delft, F. ...Bunkoczi, G. / Rellos, P. / Das, S. / Ugochukwu, E. / Fedorov, O. / Sobott, F. / Eswaran, J. / Amos, A. / Ball, L. / von Delft, F. / Bullock, A. / Debreczeni, J. / Turnbull, A. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: The Structure of Casein Kinase 1 Gamma 2
Authors: Bunkoczi, G. / Rellos, P. / Das, S. / Ugochukwu, E. / Fedorov, O. / Sobott, F. / Eswaran, J. / Amos, A. / Ball, L. / von Delft, F. / Bullock, A. / Debreczeni, J. / Turnbull, A. / Sundstrom, ...Authors: Bunkoczi, G. / Rellos, P. / Das, S. / Ugochukwu, E. / Fedorov, O. / Sobott, F. / Eswaran, J. / Amos, A. / Ball, L. / von Delft, F. / Bullock, A. / Debreczeni, J. / Turnbull, A. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Knapp, S.
History
DepositionOct 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 22, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / 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 1.5Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 GAMMA 2 ISOFORM
B: CASEIN KINASE 1 GAMMA 2 ISOFORM
C: CASEIN KINASE 1 GAMMA 2 ISOFORM
D: CASEIN KINASE 1 GAMMA 2 ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,98510
Polymers146,3684
Non-polymers1,6176
Water3,729207
1
A: CASEIN KINASE 1 GAMMA 2 ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9842
Polymers36,5921
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CASEIN KINASE 1 GAMMA 2 ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0093
Polymers36,5921
Non-polymers4162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CASEIN KINASE 1 GAMMA 2 ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0093
Polymers36,5921
Non-polymers4162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: CASEIN KINASE 1 GAMMA 2 ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9842
Polymers36,5921
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.959, 97.088, 185.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A42 - 338
2112B42 - 338
3112C42 - 338
4112D42 - 338

NCS oper:
IDCodeMatrixVector
1given(-0.16103, 0.62818, 0.76122), (0.62394, -0.5328, 0.57168), (0.7647, 0.56702, -0.30615)-23.20744, 24.83066, 5.21805
2given(-0.26053, -0.06503, 0.96327), (-0.07143, -0.9937, -0.0864), (0.96282, -0.09131, 0.25424)-39.83032, 68.93835, -36.5856
3given(0.72221, -0.69167, -0.0024), (0.41943, 0.43519, 0.79667), (-0.54999, -0.57638, 0.6044)-1.57685, -57.77915, 25.86202

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Components

#1: Protein
CASEIN KINASE 1 GAMMA 2 ISOFORM / CKI-GAMMA 2


Mass: 36592.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P78368, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13IN4O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCYS111 OXIDIZED

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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 Å3/Da / Density % sol: 59 %
Crystal growpH: 6.5
Details: 0.1 M NACACOD PH=6.5 20% PEG10K 0.2 M MGCL2, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2005
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.48 Å / Num. obs: 66823 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.04 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.93
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.39 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2CSN

2csn


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 20.597 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3383 5.1 %RANDOM
Rwork0.208 ---
obs0.211 63360 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å20 Å2
2--4.57 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9242 0 82 207 9531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229591
X-RAY DIFFRACTIONr_bond_other_d0.0020.028652
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.98513013
X-RAY DIFFRACTIONr_angle_other_deg0.85319943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41751147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15922.778432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.093151567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7961566
X-RAY DIFFRACTIONr_chiral_restr0.0760.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210527
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022067
X-RAY DIFFRACTIONr_nbd_refined0.2010.22013
X-RAY DIFFRACTIONr_nbd_other0.1820.28595
X-RAY DIFFRACTIONr_nbtor_refined0.1850.24664
X-RAY DIFFRACTIONr_nbtor_other0.090.25584
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3390.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.21135793
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.54459272
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.98984249
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.348113739
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1654tight positional0.050.05
2B1654tight positional0.050.05
3C1654tight positional0.040.05
4D1654tight positional0.040.05
1A2462medium positional0.590.5
2B2462medium positional0.560.5
3C2462medium positional0.560.5
4D2462medium positional0.60.5
1A1654tight thermal0.110.5
2B1654tight thermal0.140.5
3C1654tight thermal0.090.5
4D1654tight thermal0.090.5
1A2462medium thermal0.882
2B2462medium thermal1.172
3C2462medium thermal0.772
4D2462medium thermal0.792
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 224
Rwork0.315 4267
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)
12.2121.2459-0.10891.6953-0.6510.3553-0.04220.31290.0909-0.50040.0292-0.2022-0.1178-0.0230.0129-0.15220.0089-0.0064-0.05790.0057-0.13083.480638.38967.6224
21.5491.0311.41530.72741.33154.97260.07120.01520.2231-0.19220.0565-0.0195-0.40020.1432-0.1277-0.23030.0088-0.0057-0.0412-0.0581-0.2269-0.481639.272822.2269
32.29750.1153-1.0950.97870.33671.46170.0079-0.26610.1588-0.0285-0.0530.1154-0.1490.06820.0451-0.24810.01060.0052-0.0241-0.1168-0.285-8.291235.698534.8545
45.849-2.19830.18263.17912.3997.2284-0.0863-0.6212-0.75880.4826-0.01690.79990.7157-0.7550.1031-0.1483-0.00070.0543-0.10860.0803-0.17166.068810.963927.2683
53.01231.5206-0.20264.03740.95471.2629-0.1437-0.5405-0.15370.1330.02580.07520.016-0.13670.1179-0.29350.04490.0533-0.31050.0168-0.287218.673416.128220.783
61.9971-0.2209-0.05721.4473-0.50941.9354-0.03980.1078-0.0879-0.2181-0.0201-0.08950.09720.20590.0599-0.2757-0.0259-0.0181-0.37860.0011-0.277827.070920.37648.486
75.8433-0.2882-3.04040.95150.05725.0653-0.43360.9871-0.6749-0.1295-0.47150.55260.1456-1.40630.90510.1716-0.44310.20640.8275-0.60150.315833.927723.542755.4645
86.7431-1.2499-0.38090.8931-0.08165.776-0.70340.4372-1.02190.2403-0.23820.54521.0831-0.96190.94160.1287-0.30950.31650.1575-0.34970.251349.161921.915455.6957
93.1057-1.0312-1.97891.16620.98663.7696-0.39550.0897-0.57910.253-0.11620.35040.9075-0.19310.5117-0.0441-0.06840.132-0.0588-0.1791-0.080263.217924.795651.2684
105.4313-0.34590.75032.75980.92360.4483-0.03870.77790.2401-0.5145-0.26210.3313-0.0516-0.26270.3008-0.1929-0.03680.0068-0.0727-0.153-0.089754.129149.120865.6394
113.4212-0.4573-3.03622.0337-2.35588.4974-0.17480.29220.05720.17040.05990.0553-0.0371-0.49850.1149-0.2447-0.08310.0896-0.1179-0.1850.018343.635443.318575.3886
122.2822-0.1396-0.90641.45590.43363.4475-0.27410.626-0.38970.0819-0.2490.33880.4232-1.1340.5231-0.1777-0.18690.14170.2743-0.27490.058529.858140.0780.4751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 81
2X-RAY DIFFRACTION1A101 - 122
3X-RAY DIFFRACTION2A82 - 100
4X-RAY DIFFRACTION2A123 - 136
5X-RAY DIFFRACTION2A166 - 190
6X-RAY DIFFRACTION3A137 - 165
7X-RAY DIFFRACTION3A191 - 338
8X-RAY DIFFRACTION4B44 - 81
9X-RAY DIFFRACTION4B101 - 122
10X-RAY DIFFRACTION5B82 - 100
11X-RAY DIFFRACTION5B123 - 136
12X-RAY DIFFRACTION5B166 - 190
13X-RAY DIFFRACTION6B137 - 165
14X-RAY DIFFRACTION6B191 - 338
15X-RAY DIFFRACTION7C46 - 81
16X-RAY DIFFRACTION7C101 - 122
17X-RAY DIFFRACTION8C82 - 100
18X-RAY DIFFRACTION8C123 - 136
19X-RAY DIFFRACTION8C166 - 190
20X-RAY DIFFRACTION9C137 - 165
21X-RAY DIFFRACTION9C191 - 337
22X-RAY DIFFRACTION10D42 - 81
23X-RAY DIFFRACTION10D101 - 122
24X-RAY DIFFRACTION11D82 - 100
25X-RAY DIFFRACTION11D123 - 136
26X-RAY DIFFRACTION11D166 - 190
27X-RAY DIFFRACTION12D137 - 165
28X-RAY DIFFRACTION12D191 - 338

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