+Open data
-Basic information
Entry | Database: PDB / ID: 7bax | ||||||
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Title | Crystal structure of LYS11 ectodomain | ||||||
Components | LysM type receptor kinase | ||||||
Keywords | PLANT PROTEIN / LysM-RLK ectodomain | ||||||
Function / homology | Function and homology information membrane => GO:0016020 / protein kinase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Lotus japonicus (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Laursen, M. / Cheng, J. / Gysel, K. / Blaise, M. / Andersen, K.R. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bax.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bax.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bax_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 7bax_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 7bax_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7bax_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/7bax ftp://data.pdbj.org/pub/pdb/validation_reports/ba/7bax | HTTPS FTP |
-Related structure data
Related structure data | 7au7SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.41 Å3/Da / Density % sol: 72.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Sodium malonate pH 6.0, 12% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.954 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→38.08 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.4765223404 Å / Origin y: -48.8526891223 Å / Origin z: -8.57149754329 Å
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Refinement TLS group | Selection details: all |