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- PDB-9h3a: Crystal structure of Lotus japonicus CHIP13 extracellular domain ... -

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Basic information

Entry
Database: PDB / ID: 9h3a
TitleCrystal structure of Lotus japonicus CHIP13 extracellular domain in complex with chitooctaose
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / Chitin / receptor kinase / plant immunity / complex
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
LysM type receptor kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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
DepositionOct 16, 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 type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8146
Polymers25,0091
Non-polymers2,8065
Water6,864381
1
hetero molecules

hetero molecules

A: LysM type receptor kinase
hetero molecules

A: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,62912
Polymers50,0172
Non-polymers5,61110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
crystal symmetry operation3_444x-1/2,y-1/2,z-11
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area6290 Å2
ΔGint40 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.750, 45.550, 75.560
Angle α, β, γ (deg.)90.000, 102.261, 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-475-

HOH

21A-657-

HOH

31A-756-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LysM type receptor kinase


Mass: 25008.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Strain: Gifu / Gene: LYS13 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3KU00

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Sugars , 3 types, 4 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 2 types, 382 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion
Details: 0.2M Ammonium chloride 20% w/vPEG 3350 1 mM octa-N-acetyl-chitooctaose

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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: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.35→39.45 Å / Num. obs: 110107 / % possible obs: 95.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.03 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rrim(I) all: 0.062 / Net I/σ(I): 15.04
Reflection shellResolution: 1.35→1.39 Å / Mean I/σ(I) obs: 0.32 / Num. unique obs: 4354 / CC1/2: 0.51 / Rrim(I) all: 8.77

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→39.45 Å / SU ML: 0.3247 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1913 2462 4.41 %
Rwork0.1529 53350 -
obs0.1546 55812 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 189 381 2324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01592061
X-RAY DIFFRACTIONf_angle_d1.5652838
X-RAY DIFFRACTIONf_chiral_restr0.1113368
X-RAY DIFFRACTIONf_plane_restr0.0124351
X-RAY DIFFRACTIONf_dihedral_angle_d12.3171970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.381.58741221.74372630X-RAY DIFFRACTION84.11
1.38-1.40.85331330.82292856X-RAY DIFFRACTION90.96
1.4-1.430.51741290.45562832X-RAY DIFFRACTION92.39
1.43-1.470.38871360.31172951X-RAY DIFFRACTION93.04
1.47-1.50.34821330.2922903X-RAY DIFFRACTION93.82
1.5-1.550.32681360.28632949X-RAY DIFFRACTION94.05
1.55-1.590.26521370.19042938X-RAY DIFFRACTION94.41
1.59-1.640.21811370.14732965X-RAY DIFFRACTION95.01
1.64-1.70.18761370.13292961X-RAY DIFFRACTION95.18
1.7-1.770.19551390.12753007X-RAY DIFFRACTION95.22
1.77-1.850.17021380.12322974X-RAY DIFFRACTION94.96
1.85-1.950.17291350.12332967X-RAY DIFFRACTION95.5
1.95-2.070.18071420.11953042X-RAY DIFFRACTION96.43
2.07-2.230.16161400.11913037X-RAY DIFFRACTION97.16
2.23-2.450.17421420.1283083X-RAY DIFFRACTION97.34
2.45-2.810.15791410.1363049X-RAY DIFFRACTION97.2
2.81-3.540.18621400.13663057X-RAY DIFFRACTION95.83
3.54-39.450.16851450.15363149X-RAY DIFFRACTION97.05

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