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- PDB-7nx1: TG domain of LTK -

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Basic information

Entry
Database: PDB / ID: 7nx1
TitleTG domain of LTK
ComponentsLeukocyte tyrosine kinase receptor
KeywordsPROTEIN BINDING / Cell Surface Receptor Cytokine binding
Function / homology
Function and homology information


: / receptor signaling protein tyrosine kinase activator activity / positive regulation of kinase activity / regulation of neuron differentiation / positive regulation of cardiac muscle cell apoptotic process / peptidyl-tyrosine autophosphorylation / cellular response to retinoic acid / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase ...: / receptor signaling protein tyrosine kinase activator activity / positive regulation of kinase activity / regulation of neuron differentiation / positive regulation of cardiac muscle cell apoptotic process / peptidyl-tyrosine autophosphorylation / cellular response to retinoic acid / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / positive regulation of neuron projection development / regulation of cell population proliferation / protein tyrosine kinase activity / cell population proliferation / receptor complex / protein kinase activity / protein phosphorylation / negative regulation of apoptotic process / signal transduction / ATP binding / membrane / plasma membrane
Similarity search - Function
Leukocyte tyrosine kinase receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site ...Leukocyte tyrosine kinase receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
Similarity search - Domain/homology
TERBIUM(III) ION / Leukocyte tyrosine kinase receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsDe Munck, S. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Nature / Year: 2021
Title: Structural basis of cytokine-mediated activation of ALK family receptors.
Authors: De Munck, S. / Provost, M. / Kurikawa, M. / Omori, I. / Mukohyama, J. / Felix, J. / Bloch, Y. / Abdel-Wahab, O. / Bazan, J.F. / Yoshimi, A. / Savvides, S.N.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukocyte tyrosine kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1247
Polymers32,0701
Non-polymers1,0546
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-16 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.040, 54.460, 55.010
Angle α, β, γ (deg.)90.000, 111.284, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Leukocyte tyrosine kinase receptor / Protein tyrosine kinase 1


Mass: 32069.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTK, TYK1 / Production host: Homo sapiens (human)
References: UniProt: P29376, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: MOPSO/Bis-Tris pH 6.3 12% PEG 20000 25% Trimethyl propane 2% w/v NDSB 195 5mM YCl3 . 6H2O 5mM ErCl3 . 6H2O 5mM TbCl3 . 6H2O 5mM YbCl3 . 6H2O

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→51.26 Å / Num. obs: 145183 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.14 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 1.3→1.38 Å / Num. unique obs: 23510 / CC1/2: 0.55 / Rrim(I) all: 1.26

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→51.26 Å / SU ML: 0.1347 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.2737
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1805 2880 1.98 %RANDOM
Rwork0.1594 142263 --
obs0.1598 145143 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.39 Å2
Refinement stepCycle: LAST / Resolution: 1.3→51.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 32 173 2128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682097
X-RAY DIFFRACTIONf_angle_d1.09752845
X-RAY DIFFRACTIONf_chiral_restr0.0793276
X-RAY DIFFRACTIONf_plane_restr0.0065395
X-RAY DIFFRACTIONf_dihedral_angle_d15.133733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.30921250.3226129X-RAY DIFFRACTION89.57
1.32-1.340.36021360.30246802X-RAY DIFFRACTION98.08
1.34-1.370.28671440.27676752X-RAY DIFFRACTION99.54
1.37-1.390.29571370.26346827X-RAY DIFFRACTION99.5
1.39-1.420.3081410.24176859X-RAY DIFFRACTION99.4
1.42-1.450.25661420.23586816X-RAY DIFFRACTION99.36
1.45-1.490.21151380.2166837X-RAY DIFFRACTION99.13
1.49-1.520.22011340.1966791X-RAY DIFFRACTION98.83
1.52-1.560.21461400.17576711X-RAY DIFFRACTION98.43
1.56-1.610.16491400.14976866X-RAY DIFFRACTION99.59
1.61-1.660.15431320.14216728X-RAY DIFFRACTION99.54
1.66-1.720.17021400.13776953X-RAY DIFFRACTION99.41
1.72-1.790.13531360.13016756X-RAY DIFFRACTION99.39
1.79-1.870.15751310.12346779X-RAY DIFFRACTION98.93
1.87-1.970.13811430.12026776X-RAY DIFFRACTION98.79
1.97-2.10.15761330.11726818X-RAY DIFFRACTION99.56
2.1-2.260.14831320.12016806X-RAY DIFFRACTION99.54
2.26-2.480.13871420.13536862X-RAY DIFFRACTION99.59
2.48-2.840.17021440.1546787X-RAY DIFFRACTION98.86
2.84-3.580.16891340.14766825X-RAY DIFFRACTION99.57
3.58-51.260.20221360.18116783X-RAY DIFFRACTION99

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