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- PDB-9gxz: Structure of the Medicago truncatula LYR4 ectodomain -

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Basic information

Entry
Database: PDB / ID: 9gxz
TitleStructure of the Medicago truncatula LYR4 ectodomain
ComponentsLysM-domain receptor-like kinase
KeywordsPLANT PROTEIN
Function / homology
Function and homology information


response to other organism / protein kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / : / NFP/LYK LysM1 domain / LYK4/5 LysM3 domain / : / : / LYK3/4/5 LysM2 domain / Lysin motif / LysM domain superfamily / LysM domain profile. ...: / : / NFP/LYK LysM1 domain / LYK4/5 LysM3 domain / : / : / LYK3/4/5 LysM2 domain / Lysin motif / LysM domain superfamily / LysM domain profile. / LysM domain / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
LysM-domain receptor-like kinase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRuebsam, H. / Gysel, K. / Andersen, K.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
The Carlsberg Foundation Denmark
Danish Council for Independent Research Denmark
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Structural basis for size-selective perception of chitin in plants
Authors: Gysel, K. / Hansen, S.B. / Ruebsam, H. / Alsarraf, H.M.A.B. / Madland, E. / Cheng, J.X.J. / Baadegaard, C. / Poulsen, E.C. / Vinther, M. / Fort, S. / Stougaard, J. / Andersen, K.R.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysM-domain receptor-like kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,65922
Polymers27,2301
Non-polymers2,42821
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-6 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.247, 80.438, 46.898
Angle α, β, γ (deg.)90.000, 90.310, 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 LysM-domain receptor-like kinase


Mass: 27230.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11433363, MTR_5g085790, MtrunA17_Chr5g0439331 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G7K7K0
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2M Ammonium sulfate, 0.1 M Bis-Tris buffer pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→40.22 Å / Num. obs: 37799 / % possible obs: 98.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.84 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.22
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 3459 / CC1/2: 0.453

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.22 Å / SU ML: 0.1742 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.4622
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1833 1887 4.98 %
Rwork0.1464 35999 -
obs0.1483 37797 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 149 237 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01581963
X-RAY DIFFRACTIONf_angle_d1.44262688
X-RAY DIFFRACTIONf_chiral_restr0.1231331
X-RAY DIFFRACTIONf_plane_restr0.0107338
X-RAY DIFFRACTIONf_dihedral_angle_d14.943737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.29611360.2692464X-RAY DIFFRACTION87.6
1.54-1.580.26541340.2362692X-RAY DIFFRACTION96.85
1.58-1.630.25791500.19922802X-RAY DIFFRACTION99.9
1.63-1.690.22531320.17422813X-RAY DIFFRACTION99.76
1.69-1.760.23251630.1642762X-RAY DIFFRACTION99.8
1.76-1.840.2151520.16242783X-RAY DIFFRACTION99.9
1.84-1.940.18681520.12832801X-RAY DIFFRACTION99.8
1.94-2.060.17211470.11882814X-RAY DIFFRACTION99.83
2.06-2.220.1831260.11962800X-RAY DIFFRACTION99.93
2.22-2.440.15251530.12892805X-RAY DIFFRACTION99.56
2.44-2.790.18721580.14282784X-RAY DIFFRACTION99.53
2.8-3.520.16131340.14512841X-RAY DIFFRACTION99.66
3.52-40.220.16541500.14252838X-RAY DIFFRACTION99.37

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