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- PDB-9q83: Crystal structure of Lotus japonicus CHIP13 in complex with chito... -

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Basic information

Entry
Database: PDB / ID: 9q83
TitleCrystal structure of Lotus japonicus CHIP13 in complex with chitooctaose
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / LysM / Chitin / Plant immunity
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 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
ACETATE ION / IMIDAZOLE / LysM type receptor kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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
E: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,83218
Polymers54,2322
Non-polymers7,60016
Water5,639313
1
A: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,07810
Polymers27,1161
Non-polymers3,9629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7548
Polymers27,1161
Non-polymers3,6387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.786, 70.751, 91.984
Angle α, β, γ (deg.)90.000, 117.935, 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

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Components

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Protein , 1 types, 2 molecules AE

#1: Protein LysM type receptor kinase


Mass: 27115.969 Da / Num. of mol.: 2
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 , 5 types, 10 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.: 2
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 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: 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.: 3
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#10: 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 , 5 types, 319 molecules

#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.15M LiSO4, 0.075 M NaAc pH 4.5 22.5% PEG-8000

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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: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.01→80.398 Å / Num. obs: 25349 / % possible obs: 51.6 % / Redundancy: 7 % / Biso Wilson estimate: 23.03 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.096 / Rrim(I) all: 0.256 / Net I/σ(I): 7.3
Reflection shellResolution: 2.024→2.3 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1267 / CC1/2: 0.597 / Rpim(I) all: 0.494 / Rrim(I) all: 1.312

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→64.2 Å / SU ML: 0.2298 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2435 1289 5.09 %
Rwork0.205 24047 -
obs0.207 25336 50.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.14 Å2
Refinement stepCycle: LAST / Resolution: 2.01→64.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 509 313 4183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314011
X-RAY DIFFRACTIONf_angle_d0.75315502
X-RAY DIFFRACTIONf_chiral_restr0.0533746
X-RAY DIFFRACTIONf_plane_restr0.0048663
X-RAY DIFFRACTIONf_dihedral_angle_d18.03852018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.090.258640.2837121X-RAY DIFFRACTION2.25
2.1-2.190.3474250.2952432X-RAY DIFFRACTION8.24
2.19-2.310.3539330.2811730X-RAY DIFFRACTION13.73
2.31-2.450.2694640.27931212X-RAY DIFFRACTION23.08
2.45-2.640.33861120.28621999X-RAY DIFFRACTION37.91
2.64-2.910.30922020.27233731X-RAY DIFFRACTION70.09
2.91-3.330.29232750.23345079X-RAY DIFFRACTION96.19
3.33-4.190.23422850.185348X-RAY DIFFRACTION99.81
4.19-64.20.18142890.16485395X-RAY DIFFRACTION99.58
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59564485942-0.7048095370230.1059154332991.129452267710.0879172692790.170729809411-0.0685146390458-0.124377367077-0.1119985555970.2210117351520.187638520040.278039915511-0.0784716063491-0.234712208755-0.1740451727720.2546508153950.185089278230.06714081189860.3423592538410.1492342206260.288125392471-34.292265403223.67138161420.6880451789
20.91515113573-0.0294183067698-0.6634883314180.552944515955-0.3739535643261.223590269410.0412138567380.1437029976030.03697160406040.1128222441080.00276343976099-0.00630219837566-0.103838854068-0.177547954881-0.02870332422630.04557179620320.0399877232434-0.04935584788030.05258437206230.01143823714630.112934239028-17.548535084517.039042890216.7515244248
30.815162626716-0.1141728966881.042284317531.3414454134-1.26240876944.986201365920.1635338457950.101781460691-0.08762435818050.0361706944734-0.03398756271560.07109334903010.347935499653-0.230491099529-0.1788819831870.0580586813329-0.0192450270345-0.06817884394340.1171390594970.01842385219370.203675581461-25.467974127610.681106261823.1592288109
42.19562204723-0.4216447844541.30909474692.685006762590.3710854919025.496729702210.06954963283440.2936890792780.219923117307-0.1369393343590.02579470731320.246373721503-0.21586758341-0.191514777040.002583624245520.1263633256740.123011787830.05467161091220.2941117673450.1353581209610.198986326714-23.874943942126.67359752174.88111554475
50.805596140014-0.4835887934220.09156149405190.347749389435-0.02166045865660.2311030575660.09560450937780.1761259215520.1628584882630.002841694255020.00447937073816-0.0542643392605-0.130624282419-0.124145335856-0.01390465945550.4023324138370.2850723188630.1133217181170.4365417446330.2112826166740.427781067592-27.292908753933.5770482068.75085638297
67.07082575234-0.710763680514-2.934038989441.96252717745-1.631203791174.98384211107-0.0109335731527-0.298274586880.4399806867390.150988073206-0.131208142798-0.28626848602-0.3126930698480.3272012886760.2187779849380.2282442052020.1315506397830.02306267936490.300124242470.1429919468130.251802838597-16.563314534828.66708252986.35194969039
71.03265304034-0.64103476563-0.2409910859630.4970234075180.3577413779990.498401373777-0.108890280029-0.147997110031-0.5139691654690.028607539362-0.05565590683270.2658892841170.2095952897590.1891066201770.06657392107910.1968406297420.1548962680760.05796439013730.3929965078060.1214640998710.333330519079-52.706319682330.070416823117.5350267438
81.72013600886-1.24303496179-0.4274124893121.480285424220.1223708540591.59317535927-0.153639199723-0.373370662793-0.2730368077670.1221455456510.001529619836920.01563988565430.1407286463470.1847625342980.1188378454530.05781408606050.0112455907263-0.01445379190040.1397708685440.04402459689460.140226457626-66.173309214440.41024039522.061097032
95.01799924259-0.08073683218481.453909457731.73005905786-1.942898475723.91470947878-0.255041035543-0.2592845947150.1280780657870.3008236290760.0359854676129-0.134347572619-0.3021106642030.1496076212170.2420155833730.07963552269750.035729291444-0.04427128517050.199151588814-0.002322342150630.0977328056595-54.198740113147.349942794710.2382589361
101.01611660941-0.7127312200180.2815001005691.23177739354-0.6905701851961.64442284424-0.147313491209-0.321925813667-0.3448963199910.1055864598540.07966220407380.1592955126720.172981520688-0.0229519515378-0.04975940158910.1003206772980.1783173277240.02137163584170.226474707160.1231846823530.202554435078-56.443152789134.296746636516.7582740876
110.463096167588-0.2869763880120.2346490345070.815232946037-0.2567332415590.162377830771-0.162835189437-0.317557151312-0.2069242274070.1697354410730.1162403345390.1277526527970.024381461752-0.0345753360461-0.03285561356060.38663040510.2893017352140.1224199696710.7324851047220.3461518218470.477574953746-48.688754729128.688079336731.7421198038
126.53323934673-1.90716752349-2.341869475492.33140879102-0.02709025048313.25219212347-0.377581145882-0.4723849231650.441283865720.5607090251290.348212718345-0.0561462410888-0.239822406383-0.0455422329983-0.02174194835110.3055412223350.193600038010.06009265254880.4851302497760.1957650617020.433307790814-60.366209641832.227800509933.3719510483
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 34 through 48 )AA34 - 482 - 16
22chain 'A' and (resid 49 through 157 )AA49 - 15717 - 125
33chain 'A' and (resid 158 through 182 )AA158 - 182126 - 150
44chain 'A' and (resid 183 through 203 )AA183 - 203151 - 171
55chain 'A' and (resid 204 through 234 )AA204 - 234172 - 202
66chain 'A' and (resid 235 through 251 )AA235 - 251203 - 219
77chain 'E' and (resid 34 through 69 )EQ34 - 692 - 37
88chain 'E' and (resid 70 through 130 )EQ70 - 13038 - 98
99chain 'E' and (resid 131 through 143 )EQ131 - 14399 - 111
1010chain 'E' and (resid 144 through 203 )EQ144 - 203112 - 171
1111chain 'E' and (resid 204 through 234 )EQ204 - 234172 - 202
1212chain 'E' and (resid 235 through 250 )EQ235 - 250203 - 218

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