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- PDB-9q84: Crystal structure of Lotus japonicus CHIP13 extracellular domain ... -

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Basic information

Entry
Database: PDB / ID: 9q84
TitleCrystal structure of Lotus japonicus CHIP13 extracellular domain in complex with chitooctaose
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / LysM / Chitin / Plant immunity
Function / homology
Function and homology information


protein kinase activity / ATP binding / membrane
Similarity search - Function
: / : / NFP/LYK LysM1 domain / LYK4/5 LysM3 domain / : / : / LYK3/4/5 LysM2 domain / Lysin motif / LysM domain profile. / LysM domain ...: / : / NFP/LYK LysM1 domain / LYK4/5 LysM3 domain / : / : / LYK3/4/5 LysM2 domain / Lysin motif / LysM domain profile. / LysM domain / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
IMIDAZOLE / LysM type receptor kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsGysel, 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
DepositionFeb 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,69313
Polymers27,1161
Non-polymers4,57712
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.882, 66.776, 53.203
Angle α, β, γ (deg.)90.000, 109.348, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LysM type receptor kinase


Mass: 27115.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Gene: LYS13 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3KU00

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Sugars , 4 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1643.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,8,7/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 223 molecules

#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 25% (w/v) PEG-3350

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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: P14 (MX2) / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.41→48.22 Å / Num. obs: 86273 / % possible obs: 94.32 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.08 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06422 / Rpim(I) all: 0.04014 / Rrim(I) all: 0.076 / Net I/σ(I): 7.96
Reflection shellResolution: 1.41→1.45 Å / Rmerge(I) obs: 0.9979 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 2307 / CC1/2: 0.316 / CC star: 0.693 / Rpim(I) all: 0.7904 / Rrim(I) all: 1.283

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→48.22 Å / SU ML: 0.1883 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1814 2292 5.22 %
Rwork0.1464 41625 -
obs0.1482 43917 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.55 Å2
Refinement stepCycle: LAST / Resolution: 1.41→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 308 216 2225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762108
X-RAY DIFFRACTIONf_angle_d1.13142890
X-RAY DIFFRACTIONf_chiral_restr0.0759401
X-RAY DIFFRACTIONf_plane_restr0.0071344
X-RAY DIFFRACTIONf_dihedral_angle_d15.85991074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.450.5414650.43271139X-RAY DIFFRACTION41.26
1.45-1.480.40471320.38062362X-RAY DIFFRACTION85.85
1.48-1.520.31631420.29952602X-RAY DIFFRACTION95.38
1.52-1.560.32791510.25632732X-RAY DIFFRACTION98.8
1.56-1.60.23841460.2222716X-RAY DIFFRACTION99.24
1.6-1.650.26581480.20562705X-RAY DIFFRACTION98.55
1.65-1.710.26291470.19812740X-RAY DIFFRACTION98.73
1.71-1.780.22281500.16692677X-RAY DIFFRACTION98.88
1.78-1.860.20041510.15122744X-RAY DIFFRACTION99.31
1.86-1.960.20051460.12622727X-RAY DIFFRACTION99.1
1.96-2.080.16141510.12882748X-RAY DIFFRACTION99.25
2.08-2.250.15991510.12382720X-RAY DIFFRACTION98.83
2.25-2.470.17141520.11742719X-RAY DIFFRACTION98.73
2.47-2.830.16471510.13442735X-RAY DIFFRACTION99.24
2.83-3.560.15471530.12972778X-RAY DIFFRACTION99.46
3.56-48.220.16591560.14192781X-RAY DIFFRACTION98.76

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