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

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Basic information

Entry
Database: PDB / ID: 9gxf
TitleCrystal structure of Lotus japonicus CHIP13 extracellular domain
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / Receptor / carbohydrate binding / immunity / chitin
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
ACETATE ION / LysM type receptor kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGysel, K. / Andersen, K.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0071300 Denmark
Danish Council for Independent Research3103-00137B Denmark
The Carlsberg FoundationCF21-0139 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
DepositionSep 30, 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

Downloads & links

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Assembly

Deposited unit
A: LysM type receptor kinase
B: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,94513
Polymers50,0172
Non-polymers3,92811
Water9,512528
1
A: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6137
Polymers25,0091
Non-polymers1,6046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint35 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.739, 91.902, 92.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LysM type receptor kinase


Mass: 25008.721 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 , 4 types, 8 molecules

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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}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.: 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

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Non-polymers , 3 types, 531 molecules

#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaAc . 3H2O pH 4.5 23% PEG-3350 / PH range: 4.5

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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: 1.64→49.49 Å / Num. obs: 61671 / % possible obs: 99.81 % / Redundancy: 13.5 % / Biso Wilson estimate: 27.67 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02493 / Rrim(I) all: 0.09193 / Net I/σ(I): 14.61
Reflection shellResolution: 1.64→1.68 Å / Mean I/σ(I) obs: 0.89 / Num. unique obs: 4077 / CC1/2: 0.416 / Rpim(I) all: 0.7006 / Rrim(I) all: 2.612

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→49.49 Å / SU ML: 0.2463 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 2120 3.44 %
Rwork0.1761 59522 -
obs0.177 61642 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.62 Å2
Refinement stepCycle: LAST / Resolution: 1.64→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 259 528 4143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533843
X-RAY DIFFRACTIONf_angle_d0.8675293
X-RAY DIFFRACTIONf_chiral_restr0.0515680
X-RAY DIFFRACTIONf_plane_restr0.0057665
X-RAY DIFFRACTIONf_dihedral_angle_d14.97271639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.37581360.32173942X-RAY DIFFRACTION99.98
1.68-1.720.30071300.28653876X-RAY DIFFRACTION99.65
1.72-1.770.36251460.31793935X-RAY DIFFRACTION99.88
1.77-1.820.3661400.3233912X-RAY DIFFRACTION99.93
1.82-1.880.28011410.25243936X-RAY DIFFRACTION99.63
1.88-1.940.24951410.19163911X-RAY DIFFRACTION99.9
1.94-2.020.23121400.17873942X-RAY DIFFRACTION99.88
2.02-2.110.18861420.17983931X-RAY DIFFRACTION99.93
2.11-2.230.20881390.18343944X-RAY DIFFRACTION99.76
2.23-2.370.20571390.16553987X-RAY DIFFRACTION99.85
2.37-2.550.20611450.17243986X-RAY DIFFRACTION99.93
2.55-2.80.22791440.17983978X-RAY DIFFRACTION99.95
2.8-3.210.20831420.16663989X-RAY DIFFRACTION99.85
3.21-4.040.171430.1514061X-RAY DIFFRACTION99.76
4.04-49.490.14871520.14994192X-RAY DIFFRACTION99.34
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)
15.48990576613-1.67059869431-2.411920666673.904484209070.9297849322585.36911172053-0.02843599669370.71861841016-0.0564143119319-0.265042821169-0.04302355596060.0490634003956-0.0964879876665-0.2349870029840.1123238544760.275119339708-0.0208243526087-0.03384938757530.363008987211-0.008806838313530.257326152931-13.214353503-12.7265448103-4.99803429545
23.58401827784-2.81030681255-0.5070427278784.274684906481.071710667275.450805872940.0392880748243-0.05437580202470.216785367642-0.0528612724086-0.02063855805060.0387747401875-0.602107967518-0.399073625871-0.06622280560380.149638782534-0.0317644712194-0.03347182381360.209686372304-0.02798456467270.264089936684-14.2528296857-5.541241903698.30853590536
31.75735775003-0.2198663577240.5073907690891.81765784249-0.6753097390272.95287545113-0.0133206336733-0.189962808327-0.03816592289930.0280540401408-0.0033613118232-0.0367180469514-0.01991672546130.01170833519830.0148611960750.14720453652-0.0255964531696-0.00176114570570.221820269029-0.01388847005750.219028272137-6.74966730898-13.809464351917.5744716497
43.61941203908-2.05863284757-1.269918428092.142786094830.8563322918112.830919077810.0699919293698-0.0399265554810.183323633621-0.206415356118-0.077922302601-0.175878233803-0.1993683915230.2633905851840.006656915705790.173518347197-0.04011298069560.002537076914270.194259064940.01035531368280.203723804976-0.7538643941-12.11507697363.18498472088
51.03895491893-0.104158929952-0.08259539447354.081769502241.336142969843.98247668580.05153616416490.0200189417116-0.114068642292-0.0760465551888-0.1396115013620.284069776311-0.0337599118644-0.6453150481220.1093649470570.14487512832-0.00231774444385-0.01574649467720.362397217554-0.03291822181590.265805900226-25.2153497675-13.89550805777.73812694822
65.24199378296-0.765917145082-2.201638067721.540588970760.9649185415578.49133488137-0.0249574972571-0.149815658778-0.3513037270940.0515060289416-0.09659327580290.01338816047840.199172562968-0.695752421745-0.006121237124710.162836684673-0.0535823574629-0.01372536350360.316603959219-0.01939641124150.320443683266-21.8620425254-15.200341361617.0395172194
73.777311366211.0020661943-1.631629901133.9114712692-1.372679014995.22520535904-0.00556861755994-0.486500820378-0.09854329403340.316850176978-0.146331377020.01103539943270.0651660355496-0.007991742809690.1196662803370.24207014027-0.00835556419739-0.01734080095360.296046515964-0.007460184007410.2652155968715.4466328013-12.973743436350.6636930006
83.084049581812.029958261950.4104122280323.09546713427-0.6828192531233.05303882242-0.05689524165710.1028429158160.2975856497530.00113267762637-0.03748504601440.0633366571401-0.3007109192770.284165123580.09205533554050.09871234749310.017359596887-0.0180720091840.1891608247920.02823687064310.29471547050916.8672985464-5.6036019502536.6555592373
93.442252399260.06667474920960.6003360588144.630948701520.4868904609323.945875323210.007907403816550.373893148858-0.0996077375683-0.117857292179-0.003127279723770.008342622609490.2125987829120.0725042710143-0.002727183302230.1435446472780.0175686294783-0.01523936007620.247014982575-0.011036241490.1909324906797.86966292649-18.287379135724.1834477962
101.847948368160.610785915728-0.3510273460470.941900367-0.1407489290532.121792298070.00807664543174-0.01165574060440.1278975402910.051482537535-0.07641597953850.06910807040310.0310907797094-0.08256851479520.05673493791620.1376767788320.0157927566144-0.004818998556840.1922563133820.0005132871902150.2532359482956.38619242373-10.767927551837.4526981201
114.597750082061.225788260460.01008610280081.58495312286-0.009757006713661.308262750050.0963135708783-0.1936725213870.3421596971010.172274174614-0.09271241943440.235575112773-0.0427889652806-0.138423790392-0.005486127940750.1683005546950.001394433718050.0241564644650.198029126623-0.009214201965490.2333461486543.80949385423-9.5800608662942.5323751253
124.135808871081.22460772371-0.2108072411015.8003063938-1.198094303733.101064044070.03755177886360.0519695185947-0.0374775931901-0.141859279548-0.205244433298-0.5022044384580.1357310073460.6028981142630.1374580806980.1575568769250.04223374241670.01495297365710.3388552391010.04863373798320.26962317377528.0989611781-13.352840660935.1396974017
135.399437708232.46792232916-3.320320842227.84792659547-0.4429467442963.9768940824-0.01177855550840.187130036986-0.1117724796840.280069197293-0.02070534618580.0225104441970.2268130533430.1878856589860.02093061348380.2597576346520.0460314816131-0.01204033689210.2620478651180.02245641406040.31889220876925.346307804-18.689149567146.0917751565
145.09566658208-0.79867692849-1.916115054521.344929493280.9360418210288.811624548480.02186982678030.573771352252-0.135406164114-0.02187001907-0.0956070459927-0.0419326748640.4802340932170.3857842049110.03315826161430.2032988091710.0578632624926-0.01027994257060.3251850050350.01975881044610.30290150492323.9837898189-15.722880352728.4858445002
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 69 )AA49 - 6917 - 37
33chain 'A' and (resid 70 through 130 )AA70 - 13038 - 98
44chain 'A' and (resid 131 through 182 )AA131 - 18299 - 150
55chain 'A' and (resid 183 through 234 )AA183 - 234151 - 202
66chain 'A' and (resid 235 through 250 )AA235 - 250203 - 218
77chain 'B' and (resid 34 through 48 )BJ34 - 482 - 16
88chain 'B' and (resid 49 through 69 )BJ49 - 6917 - 37
99chain 'B' and (resid 70 through 108 )BJ70 - 10838 - 76
1010chain 'B' and (resid 109 through 143 )BJ109 - 14377 - 111
1111chain 'B' and (resid 144 through 182 )BJ144 - 182112 - 150
1212chain 'B' and (resid 183 through 222 )BJ183 - 222151 - 190
1313chain 'B' and (resid 223 through 234 )BJ223 - 234191 - 202
1414chain 'B' and (resid 235 through 250 )BJ235 - 250203 - 218

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