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- PDB-1z57: Crystal structure of human CLK1 in complex with 10Z-Hymenialdisine -

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Basic information

Entry
Database: PDB / ID: 1z57
TitleCrystal structure of human CLK1 in complex with 10Z-Hymenialdisine
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / protein tyrosine kinase / dual specificity / splicing / human / 10Z-Hymendialdisine / Structural Genomics / Structural Genomics Consortium / SGC
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 / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / 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
DEBROMOHYMENIALDISINE / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDebreczeni, J. / Das, S. / Knapp, S. / Bullock, A. / Guo, K. / Amos, A. / Fedorov, O. / Edwards, A. / Sundstrom, M. / von Delft, F. ...Debreczeni, J. / Das, S. / Knapp, S. / Bullock, A. / Guo, K. / Amos, A. / Fedorov, O. / Edwards, A. / Sundstrom, M. / von Delft, F. / Niesen, F.H. / Ball, L. / Sobott, F. / Arrowsmith, C. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2009
Title: Kinase domain insertions define distinct roles of CLK kinases in SR protein phosphorylation.
Authors: Bullock, A.N. / Das, S. / Debreczeni, J.E. / Rellos, P. / Fedorov, O. / Niesen, F.H. / Guo, K. / Papagrigoriou, E. / Amos, A.L. / Cho, S. / Turk, B.E. / Ghosh, G. / Knapp, S.
History
DepositionMar 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Other
Revision 1.4Aug 29, 2012Group: Database references
Revision 1.5Aug 23, 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_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_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 CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8272
Polymers39,5821
Non-polymers2451
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.277, 64.434, 80.112
Angle α, β, γ (deg.)90.00, 119.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 39581.512 Da / Num. of mol.: 1 / Fragment: residues 148-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: clk1 / Plasmid: hclk1-pLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P49759, dual-specificity kinase
#2: Chemical ChemComp-DBQ / DEBROMOHYMENIALDISINE


Mass: 245.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 1.8 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEG 6K, Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 45196 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.75 Å / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JOW.pdb

1jow


Resolution: 1.7→29.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.544 / SU ML: 0.054 / Isotropic thermal model: anisotropic B-factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18581 2173 5.1 %RANDOM
Rwork0.13765 ---
obs0.14014 40775 95.01 %-
all-40775 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20.46 Å2
2---0.58 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 18 401 3093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212781
X-RAY DIFFRACTIONr_bond_other_d0.0010.022490
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9493771
X-RAY DIFFRACTIONr_angle_other_deg0.84535770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8423.333132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53215473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0281517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02593
X-RAY DIFFRACTIONr_nbd_refined0.2210.2591
X-RAY DIFFRACTIONr_nbd_other0.1790.22533
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21377
X-RAY DIFFRACTIONr_nbtor_other0.0840.21478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3250.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.67951816
X-RAY DIFFRACTIONr_mcbond_other2.1615672
X-RAY DIFFRACTIONr_mcangle_it4.3572706
X-RAY DIFFRACTIONr_scbond_it5.21691227
X-RAY DIFFRACTIONr_scangle_it6.814151064
X-RAY DIFFRACTIONr_rigid_bond_restr2.63435975
X-RAY DIFFRACTIONr_sphericity_free7.0323402
X-RAY DIFFRACTIONr_sphericity_bonded3.69635200
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 99 -
Rwork0.144 1896 -
obs--59.95 %

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