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- PDB-9h24: Crystal structure of MtCERK1 extracellular domain -

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Basic information

Entry
Database: PDB / ID: 9h24
TitleCrystal structure of MtCERK1 extracellular domain
ComponentsLysM receptor kinase K1B
KeywordsPLANT PROTEIN / Receptor / chitin / LysM
Function / homology
Function and homology information


transmembrane receptor protein kinase activity / non-specific serine/threonine protein kinase / innate immune response / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
LysM domain / LysM domain receptor kinase CERK1/LYK3-like / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...LysM domain / LysM domain receptor kinase CERK1/LYK3-like / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Similarity search - Domain/homology
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsHansen, S.B. / Gysel, K. / Andersen, K.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
The Carlsberg FoundationCF21-0139 Denmark
Danish Council for Independent Research3103-00137B Denmark
Novo Nordisk FoundationNNF21OC0071300 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 10, 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 receptor kinase K1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9095
Polymers23,0241
Non-polymers8854
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint15 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.669, 70.669, 95.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein LysM receptor kinase K1B


Mass: 23024.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11442199, MTR_3g080050, MtrunA17_Chr3g0119241 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G7J6P5
#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.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris 8.5, 40 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Oct 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.98→44.25 Å / Num. obs: 5282 / % possible obs: 99.87 % / Redundancy: 14.2 % / Biso Wilson estimate: 70.6 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rpim(I) all: 0.1823 / Net I/σ(I): 4.97
Reflection shellResolution: 2.984→3.76 Å / Num. unique obs: 2560 / CC1/2: 0.47 / Rpim(I) all: 0.6973

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→44.25 Å / SU ML: 0.4289 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2842 260 4.92 %
Rwork0.2309 5022 -
obs0.2333 5282 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.26 Å2
Refinement stepCycle: LAST / Resolution: 2.98→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 56 10 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291597
X-RAY DIFFRACTIONf_angle_d0.59642177
X-RAY DIFFRACTIONf_chiral_restr0.0493255
X-RAY DIFFRACTIONf_plane_restr0.0055284
X-RAY DIFFRACTIONf_dihedral_angle_d11.8248639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.760.33121390.29862422X-RAY DIFFRACTION99.88
3.76-44.250.261210.20342600X-RAY DIFFRACTION99.85

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