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- PDB-9gmp: TKUL kinase domain from Leishmania mexicana -

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Basic information

Entry
Database: PDB / ID: 9gmp
TitleTKUL kinase domain from Leishmania mexicana
ComponentsUncharacterized protein (Map kinase kinase-like protein)
KeywordsSIGNALING PROTEIN / Kinase domain / phosphorylation
Function / homology
Function and homology information


ubiquitin-protein transferase activity / protein serine/threonine kinase activity / ATP binding / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Tetratricopeptide repeat / TPR repeat profile. ...: / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein (Map kinase kinase-like protein)
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsFokkens, T.J. / Wolter, M. / Lorenz, S.
Funding supportEuropean Union, Germany, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)439-2022European Union
Max Planck Society Germany
German Research Foundation (DFG)GRK2243 Germany
CitationJournal: To Be Published
Title: Structure of the TKUL kinase domain
Authors: Fokkens, T.J. / Wolter, M. / Lorenz, S.
History
DepositionAug 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein (Map kinase kinase-like protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3466
Polymers30,8711
Non-polymers4745
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint2 kcal/mol
Surface area11760 Å2
Unit cell
Length a, b, c (Å)44.092, 74.565, 77.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Uncharacterized protein (Map kinase kinase-like protein)


Mass: 30871.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: LMXM_34_4000 / Production host: Escherichia coli (E. coli) / References: UniProt: E9B6S8
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus screen (Molecular Dimensions) condition F8 (0.12 M monosaccharides, 0.1 M buffer system 2 pH 7.5, 37% (v/v) precipitant mix 4) protein concentration of 15 mg/mL and a protein-to- ...Details: Morpheus screen (Molecular Dimensions) condition F8 (0.12 M monosaccharides, 0.1 M buffer system 2 pH 7.5, 37% (v/v) precipitant mix 4) protein concentration of 15 mg/mL and a protein-to-mother liquor ratio of 1:1. Prior to freezing, crystals were soaked with 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→44.09 Å / Num. obs: 21222 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.9
Reflection shellResolution: 1.89→1.93 Å / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1355 / CC1/2: 0.902

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→38.87 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 1100 5.2 %
Rwork0.1881 --
obs0.1903 21174 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 31 39 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051974
X-RAY DIFFRACTIONf_angle_d0.7092668
X-RAY DIFFRACTIONf_dihedral_angle_d14.903729
X-RAY DIFFRACTIONf_chiral_restr0.049293
X-RAY DIFFRACTIONf_plane_restr0.013345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.980.34171330.2712478X-RAY DIFFRACTION100
1.98-2.080.30131500.2322447X-RAY DIFFRACTION100
2.08-2.210.34941240.23812476X-RAY DIFFRACTION100
2.21-2.380.21051320.20182466X-RAY DIFFRACTION100
2.38-2.620.26071710.1992478X-RAY DIFFRACTION100
2.62-30.24491420.20692499X-RAY DIFFRACTION100
3-3.780.25111280.1842540X-RAY DIFFRACTION100
3.78-38.870.19051200.16822690X-RAY DIFFRACTION100

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