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- PDB-1wt6: Coiled-Coil domain of DMPK -

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Basic information

Entry
Database: PDB / ID: 1wt6
TitleCoiled-Coil domain of DMPK
ComponentsMyotonin-protein kinase
KeywordsTRANSFERASE / Coiled-coil / kinase activation / DMPK / molecular replacement
Function / homology
Function and homology information


regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction / muscle cell apoptotic process / regulation of skeletal muscle contraction by calcium ion signaling / myosin phosphatase regulator activity / regulation of myotube differentiation / regulation of synapse structural plasticity / nuclear envelope organization / actomyosin structure organization / nuclear outer membrane / regulation of heart contraction ...regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction / muscle cell apoptotic process / regulation of skeletal muscle contraction by calcium ion signaling / myosin phosphatase regulator activity / regulation of myotube differentiation / regulation of synapse structural plasticity / nuclear envelope organization / actomyosin structure organization / nuclear outer membrane / regulation of heart contraction / regulation of sodium ion transport / Ion homeostasis / sarcoplasmic reticulum membrane / intracellular calcium ion homeostasis / nuclear membrane / mitochondrial outer membrane / cytoskeleton / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Myotonin-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsGarcia, P. / Marino, M. / Mayans, O.
Citation
Journal: Faseb J. / Year: 2006
Title: Molecular insights into the self-assembly mechanism of dystrophia myotonica kinase
Authors: Garcia, P. / Ucurum, Z. / Bucher, R. / Svergun, D.I. / Huber, T. / Lustig, A. / Konarev, P.V. / Marino, M. / Mayans, O.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray analysis of the coiled-coil domain of dystrophia myotonica kinase
Authors: Garcia, P. / Marino, M. / Mayans, O.
History
DepositionNov 16, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myotonin-protein kinase
B: Myotonin-protein kinase
D: Myotonin-protein kinase


Theoretical massNumber of molelcules
Total (without water)27,4503
Polymers27,4503
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-65 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.083, 46.164, 143.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myotonin-protein kinase / Myotonic dystrophy protein kinase / MDPK / DM-kinase / DMK / DMPK / MT-PK


Mass: 9150.050 Da / Num. of mol.: 3 / Fragment: Wild-type coiled-coil domain of DPMK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETM-11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q09013, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris-HCl pH 7.5, 2.0M Na+/K+ tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98, 0.9793, 0.9795, 0.9392
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.97931
30.97951
40.93921
ReflectionResolution: 1.6→20 Å / Num. obs: 32044 / % possible obs: 96.3 % / Redundancy: 4.4 % / Net I/σ(I): 15
Reflection shellResolution: 1.6→1.69 Å / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.969 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27098 1712 5.1 %RANDOM
Rwork0.22797 ---
obs0.23014 32044 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.054 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å20 Å2
2---1.67 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 295 1908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211621
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9752172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8015192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15924.393107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00615333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4861527
X-RAY DIFFRACTIONr_chiral_restr0.1130.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021242
X-RAY DIFFRACTIONr_nbd_refined0.2870.2903
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21132
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2203
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.234
X-RAY DIFFRACTIONr_mcbond_it2.2131.51014
X-RAY DIFFRACTIONr_mcangle_it2.32221555
X-RAY DIFFRACTIONr_scbond_it4.0613651
X-RAY DIFFRACTIONr_scangle_it6.8264.5617
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 96 -
Rwork0.289 1765 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 0.2618 Å / Origin y: 23.7128 Å / Origin z: 13.1349 Å
111213212223313233
T-0.0276 Å2-0.0054 Å20.0127 Å2--0.0165 Å2-0.0134 Å2---0.0115 Å2
L0.0185 °2-0.0916 °2-0.0231 °2-2.2197 °21.2574 °2--0.8918 °2
S-0.0441 Å °0.0216 Å °-0.0493 Å °0.131 Å °0.0131 Å °0.0976 Å °0.0077 Å °0.0365 Å °0.0309 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 709 - 73
2X-RAY DIFFRACTION1BB2 - 685 - 71
3X-RAY DIFFRACTION1DC6 - 689 - 71

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