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- PDB-6seq: Lemur tyrosine kinase 3 (LMTK3) -

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Basic information

Entry
Database: PDB / ID: 6seq
TitleLemur tyrosine kinase 3 (LMTK3)
ComponentsSerine/threonine-protein kinase LMTK3
KeywordsTRANSFERASE / LMTK3 / kinase inhibitor / breast cancer
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / axon / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / ATP binding / metal ion binding
Similarity search - Function
Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase LMTK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRoe, S.M. / Owen, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateG1828 United Kingdom
CitationJournal: Sci Adv / Year: 2020
Title: The structure-function relationship of oncogenic LMTK3.
Authors: Ditsiou, A. / Cilibrasi, C. / Simigdala, N. / Papakyriakou, A. / Milton-Harris, L. / Vella, V. / Nettleship, J.E. / Lo, J.H. / Soni, S. / Smbatyan, G. / Ntavelou, P. / Gagliano, T. / ...Authors: Ditsiou, A. / Cilibrasi, C. / Simigdala, N. / Papakyriakou, A. / Milton-Harris, L. / Vella, V. / Nettleship, J.E. / Lo, J.H. / Soni, S. / Smbatyan, G. / Ntavelou, P. / Gagliano, T. / Iachini, M.C. / Khurshid, S. / Simon, T. / Zhou, L. / Hassell-Hart, S. / Carter, P. / Pearl, L.H. / Owen, R.L. / Owens, R.J. / Roe, S.M. / Chayen, N.E. / Lenz, H.J. / Spencer, J. / Prodromou, C. / Klinakis, A. / Stebbing, J. / Giamas, G.
History
DepositionJul 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Serine/threonine-protein kinase LMTK3


Theoretical massNumber of molelcules
Total (without water)153,8051
Polymers153,8051
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.586, 63.999, 134.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase LMTK3 / Lemur tyrosine kinase 3


Mass: 153804.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMTK3, KIAA1883, TYKLM3
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q96Q04, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: LMTK3 at 3.2 mg/ml in 20 mM Tris pH 7.5, 200 mM NaCl was crystallised with 70 mM bis-Tris Propane pH 6.5, 14 % w/v Polyethylene Glycol 3350, 14 mM Sodium/Potassium Phosphate, 30 % w/v sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→46.39 Å / Num. obs: 21507 / % possible obs: 91 % / Redundancy: 7.5 % / Biso Wilson estimate: 11.96 Å2 / CC1/2: 0.934 / Rmerge(I) obs: 0.422 / Rpim(I) all: 0.161 / Rrim(I) all: 0.455 / Net I/σ(I): 4.5 / Num. measured all: 161535 / Scaling rejects: 222
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.167.62.6641361318000.3331.0262.8751.194.1
8.91-46.396.50.1520093090.940.0570.16111.682.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.39 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.812 / SU R Cruickshank DPI: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1098 5.15 %RANDOM
Rwork0.194 ---
obs0.198 21335 89.8 %-
Displacement parametersBiso max: 119.32 Å2 / Biso mean: 25.01 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-3.673 Å20 Å20 Å2
2---6.6556 Å20 Å2
3---2.9826 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.1→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 0 354 2574
Biso mean---36.11 -
Num. residues----278
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1046SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes385HARMONIC5
X-RAY DIFFRACTIONt_it2296HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion282SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2942SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2296HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3130HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion3.39
LS refinement shellResolution: 2.1→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2308 21 4.92 %
Rwork0.2383 406 -
all0.2379 427 -
obs--77.2 %

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