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- PDB-6tw2: Re-refined crystal structure of di-phosphorylated human CLK1 in c... -

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Basic information

Entry
Database: PDB / ID: 6tw2
TitleRe-refined crystal structure of di-phosphorylated human CLK1 in complex with a novel substituted indole inhibitor
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / TYROSINE-PROTEIN KINASE / NUCLEUS
Function / homology
Function and homology information


dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
Chem-V25 / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsLoll, B. / Haltenhof, T. / Heyd, F. / Wahl, M.C.
CitationJournal: Mol.Cell / Year: 2020
Title: A Conserved Kinase-Based Body-Temperature Sensor Globally Controls Alternative Splicing and Gene Expression.
Authors: Haltenhof, T. / Kotte, A. / De Bortoli, F. / Schiefer, S. / Meinke, S. / Emmerichs, A.K. / Petermann, K.K. / Timmermann, B. / Imhof, P. / Franz, A. / Loll, B. / Wahl, M.C. / Preussner, M. / Heyd, F.
History
DepositionJan 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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
E: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0802
Polymers39,7411
Non-polymers3381
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-16 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.950, 64.108, 78.894
Angle α, β, γ (deg.)90.000, 118.170, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Dual specificity protein kinase CLK1 / CDC-like kinase 1


Mass: 39741.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Plasmid: PLIC-SGC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49759, dual-specificity kinase
#2: Chemical ChemComp-V25 / ethyl 3-[(E)-2-amino-1-cyanoethenyl]-6,7-dichloro-1-methyl-1H-indole-2-carboxylate


Mass: 338.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13Cl2N3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M SODIUM MALATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.006029 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006029 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 36979 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.61 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.92 Å / Redundancy: 3 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5380 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2VAG

2vag


Resolution: 1.8→29.27 Å / SU ML: 0.2533 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.2524
RfactorNum. reflection% reflection
Rfree0.2225 1887 5.11 %
Rwork0.1806 --
obs0.1828 36956 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 22 216 3002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783136
X-RAY DIFFRACTIONf_angle_d0.92914274
X-RAY DIFFRACTIONf_chiral_restr0.0571452
X-RAY DIFFRACTIONf_plane_restr0.0056557
X-RAY DIFFRACTIONf_dihedral_angle_d14.54041880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.36481540.33112666X-RAY DIFFRACTION99.44
1.85-1.910.2871420.27642662X-RAY DIFFRACTION99.64
1.91-1.970.26171280.22672711X-RAY DIFFRACTION100
1.97-2.040.24041540.21182665X-RAY DIFFRACTION100
2.04-2.120.24451360.20262713X-RAY DIFFRACTION100
2.12-2.220.23761270.19682717X-RAY DIFFRACTION100
2.22-2.330.24541430.18792679X-RAY DIFFRACTION100
2.33-2.480.25151530.18232684X-RAY DIFFRACTION100
2.48-2.670.21751510.18922699X-RAY DIFFRACTION100
2.67-2.940.27361480.19162692X-RAY DIFFRACTION100
2.94-3.360.25371560.1852689X-RAY DIFFRACTION100
3.36-4.240.16871510.14362734X-RAY DIFFRACTION100
4.24-29.270.17521440.15092758X-RAY DIFFRACTION99.38
Refinement TLS params.Method: refined / Origin x: 14.4105004445 Å / Origin y: 6.64873866416 Å / Origin z: 14.7635358718 Å
111213212223313233
T0.195319682529 Å20.0801888236946 Å2-0.034351977349 Å2-0.143813929224 Å2-0.0122509020665 Å2--0.120203453986 Å2
L1.28360247918 °20.346327532512 °20.0516627653389 °2-2.15185881748 °20.158422186504 °2--1.72104651632 °2
S-0.236491865468 Å °-0.1069164583 Å °-0.0476238493232 Å °-0.366564444794 Å °0.0840447517147 Å °0.0778981628532 Å °-0.285104590967 Å °-0.11142722922 Å °-0.323564032173 Å °
Refinement TLS groupSelection details: (chain 'E' and resid 0 through 484)

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