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- PDB-7bax: Crystal structure of LYS11 ectodomain -

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Basic information

Entry
Database: PDB / ID: 7bax
TitleCrystal structure of LYS11 ectodomain
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / LysM-RLK ectodomain
Function / homology
Function and homology information


membrane => GO:0016020 / protein kinase activity / ATP binding / plasma membrane
Similarity search - Function
LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic 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: 2.9 Å
AuthorsLaursen, M. / Cheng, J. / Gysel, K. / Blaise, M. / Andersen, K.R.
Funding support1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Kinetic proofreading of lipochitooligosaccharides determines signal activation of symbiotic plant receptors.
Authors: Gysel, K. / Laursen, M. / Thygesen, M.B. / Lironi, D. / Bozsoki, Z. / Hjuler, C.T. / Maolanon, N.N. / Cheng, J. / Bjork, P.K. / Vinther, M. / Madsen, L.H. / Rubsam, H. / Muszynski, A. / ...Authors: Gysel, K. / Laursen, M. / Thygesen, M.B. / Lironi, D. / Bozsoki, Z. / Hjuler, C.T. / Maolanon, N.N. / Cheng, J. / Bjork, P.K. / Vinther, M. / Madsen, L.H. / Rubsam, H. / Muszynski, A. / Ghodrati, A. / Azadi, P. / Sullivan, J.T. / Ronson, C.W. / Jensen, K.J. / Blaise, M. / Radutoiu, S. / Stougaard, J. / Andersen, K.R.
History
DepositionDec 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)30,0752
Polymers29,8531
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint2 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.940, 114.940, 59.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein LysM type receptor kinase


Mass: 29853.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Gene: LYS11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3KTZ8
#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.: 1 / 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
Has ligand of interestN

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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: 4.41 Å3/Da / Density % sol: 72.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Sodium malonate pH 6.0, 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.88→40 Å / Num. obs: 8086 / % possible obs: 77.1 % / Redundancy: 9.7 % / Biso Wilson estimate: 87.14 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.088 / Net I/σ(I): 15.97
Reflection shellResolution: 2.88→2.95 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 4.93 / Num. unique obs: 60 / CC1/2: 0.897 / Rrim(I) all: 0.472 / % possible all: 7.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata processing
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AU7

7au7


Resolution: 2.9→38.08 Å / SU ML: 0.2735 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.0944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 857 10.62 %
Rwork0.1879 7211 -
obs0.192 8068 79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 14 0 1596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731639
X-RAY DIFFRACTIONf_angle_d1.10012249
X-RAY DIFFRACTIONf_chiral_restr0.0765263
X-RAY DIFFRACTIONf_plane_restr0.0071290
X-RAY DIFFRACTIONf_dihedral_angle_d18.0455580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.080.2956320.3618247X-RAY DIFFRACTION16.62
3.09-3.320.3757770.3115859X-RAY DIFFRACTION55.81
3.32-3.660.2981920.24971486X-RAY DIFFRACTION99.94
3.66-4.190.24291630.18821538X-RAY DIFFRACTION100
4.19-5.260.18961890.14641509X-RAY DIFFRACTION100
5.27-38.080.20142040.1721572X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 14.4765223404 Å / Origin y: -48.8526891223 Å / Origin z: -8.57149754329 Å
111213212223313233
T0.288654086906 Å2-0.0233225609523 Å20.0825493246828 Å2-0.365176514706 Å2-0.0771293996788 Å2--0.303445540868 Å2
L5.93461620086 °22.63535314208 °2-0.375493171098 °2-5.43723282322 °2-0.688519526146 °2--6.85500153551 °2
S0.472864666147 Å °-0.110764184815 Å °-0.052245222686 Å °0.852362241711 Å °-0.104477357113 Å °0.318797542102 Å °-0.339682873811 Å °0.77598339455 Å °-0.236411350383 Å °
Refinement TLS groupSelection details: all

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