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- PDB-3raw: Crystal Structure of human CDC-like kinase 3 isoform in complex w... -

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Basic information

Entry
Database: PDB / ID: 3raw
TitleCrystal Structure of human CDC-like kinase 3 isoform in complex with leucettine L41
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / KINASE / TYROSINE-PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus
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-3RA / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsFilippakopoulos, P. / Fedorov, O. / King, O. / Debdab, M. / Carreaux, F. / Renault, S. / Bullock, A. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C.H. ...Filippakopoulos, P. / Fedorov, O. / King, O. / Debdab, M. / Carreaux, F. / Renault, S. / Bullock, A. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Meijer, L. / Bazureau, J.P. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of human CDC-like kinase 3 isoform with a benzo-dioxol ligand
Authors: Filippakopoulos, P. / Fedorov, O. / King, O. / Bullock, A. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionMar 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Dual specificity protein kinase CLK3
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1954
Polymers89,5802
Non-polymers6152
Water4,432246
1
A: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0972
Polymers44,7901
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0972
Polymers44,7901
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.670, 122.420, 69.280
Angle α, β, γ (deg.)90.000, 92.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALGLUGLUAA136 - 23733 - 134
211VALVALGLUGLUBB136 - 23733 - 134
112LEULEUPHEPHEAA239 - 296136 - 193
212LEULEUPHEPHEBB239 - 296136 - 193
122GLUGLUSERSERAA297 - 310194 - 207
222GLUGLUSERSERBB297 - 310194 - 207
132VALVALGLYGLYAA311 - 410208 - 307
232VALVALGLYGLYBB311 - 410208 - 307
113ASPASPARGARGAA415 - 480312 - 377
213ASPASPARGARGBB415 - 480312 - 377

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Dual specificity protein kinase CLK3 / CDC-like kinase 3


Mass: 44790.062 Da / Num. of mol.: 2 / Fragment: Residues 275-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P49761, dual-specificity kinase
#2: Chemical ChemComp-3RA / 5-(1,3-benzodioxol-5-ylmethyl)-2-(phenylamino)-4H-imidazol-4-one


Mass: 307.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.20M NaNO3 0.1M BTProp pH 7.5 20.0% PEG 3350 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 5.4 / Number: 233131 / Rsym value: 0.091 / D res high: 2.09 Å / D res low: 36.263 Å / Num. obs: 59553 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.6136.2698.310.040.043.8
4.676.6199.310.0620.0623.9
3.824.6799.110.0630.0633.9
3.33.8299.110.0660.0663.9
2.963.398.810.0890.0893.9
2.72.9698.410.1270.1273.9
2.52.797.910.1910.1913.9
2.342.597.810.2990.2993.9
2.22.3497.910.4680.4683.9
2.092.297.110.7550.7553.9
ReflectionResolution: 2.09→36.263 Å / Num. all: 60645 / Num. obs: 59553 / % possible obs: 98.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.09-2.23.90.75513383886020.75597.1
2.2-2.343.90.4681.63191181230.46897.9
2.34-2.53.90.2992.53038677190.29997.8
2.5-2.73.90.1913.92806671400.19197.9
2.7-2.963.90.1275.52605366380.12798.4
2.96-3.33.90.0897.42359560230.08998.8
3.3-3.823.90.0668.92083553380.06699.1
3.82-4.673.90.0638.91753345150.06399.1
4.67-6.613.90.0627.91357435160.06299.3
6.61-36.2633.80.0413.5734019390.0498.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.26 Å
Translation2.5 Å36.26 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 2EXE, 2EU9, 1Z57

2exe

2eu9

1z57


Resolution: 2.09→36.263 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2287 / WRfactor Rwork: 0.1875 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.87 / SU B: 8.663 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1611 / SU Rfree: 0.1498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 1988 3.3 %RANDOM
Rwork0.1809 ---
all0.1822 60691 --
obs0.1822 59520 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 123.05 Å2 / Biso mean: 45.8424 Å2 / Biso min: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-0.24 Å2
2--0.93 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5603 0 46 246 5895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215837
X-RAY DIFFRACTIONr_bond_other_d0.0010.023945
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9457908
X-RAY DIFFRACTIONr_angle_other_deg0.9233.0019517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71923.299288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86315962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7361539
X-RAY DIFFRACTIONr_chiral_restr0.0950.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021272
X-RAY DIFFRACTIONr_mcbond_it3.433491
X-RAY DIFFRACTIONr_mcbond_other1.45231410
X-RAY DIFFRACTIONr_mcangle_it4.90855610
X-RAY DIFFRACTIONr_scbond_it7.79182346
X-RAY DIFFRACTIONr_scangle_it9.579112298
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11267MEDIUM POSITIONAL0.220.5
11267MEDIUM THERMAL0.92
22361MEDIUM POSITIONAL0.150.5
22361MEDIUM THERMAL1.322
3919MEDIUM POSITIONAL0.340.5
3919MEDIUM THERMAL1.342
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 141 -
Rwork0.292 4212 -
all-4353 -
obs--97.4 %
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)
14.5626-0.7388-0.44757.0304-3.17283.8988-0.1248-0.1258-0.6616-0.3741-0.3192-0.82590.65040.38850.4440.32910.04210.07320.1677-0.04190.428887.681616.444214.9844
23.10440.1213-1.2361.65890.35563.9085-0.0264-0.18610.1256-0.0815-0.1322-0.06950.09510.28230.15870.01640.0251-0.01840.0926-0.02810.114186.3240.47720.3863
31.95780.46791.07280.91070.80214.248-0.08320.05940.5685-0.1947-0.01680.048-0.33250.19690.10.08270.0343-0.02960.0965-0.02690.284285.914750.662818.4345
46.45060.0640.10396.8418-2.0033.2274-0.0830.19750.79460.3785-0.1691-0.8719-0.42590.19450.25210.3350.0302-0.06260.11750.00310.404856.708472.231754.0112
53.5442-0.31630.44931.88120.40372.6986-0.04730.3279-0.24480.2129-0.09030.0889-0.0608-0.04790.13760.0299-0.01440.00670.0763-0.01570.068155.585148.612747.1668
62.605-0.6958-1.64372.06010.89684.0532-0.204-0.1812-0.68750.6119-0.04150.27410.53990.10920.24550.2373-0.05820.05620.11210.00160.320355.422238.17649.9443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 238
2X-RAY DIFFRACTION2A239 - 410
3X-RAY DIFFRACTION3A411 - 484
4X-RAY DIFFRACTION4B136 - 237
5X-RAY DIFFRACTION5B238 - 414
6X-RAY DIFFRACTION6B415 - 484

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