+Open data
-Basic information
Entry | Database: PDB / ID: 8web | ||||||
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Title | Crystal structure of Arabidopsis thaliana MIK2 ectodomain | ||||||
Components | MDIS1-interacting receptor like kinase 2 | ||||||
Keywords | PLANT PROTEIN / LRR receptor-like serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information indole glucosinolate biosynthetic process / positive regulation of defense response / pollen tube / pollen tube guidance / response to herbivore / defense response to insect / peptide receptor activity / jasmonic acid biosynthetic process / cellular response to peptide / plasmodesma ...indole glucosinolate biosynthetic process / positive regulation of defense response / pollen tube / pollen tube guidance / response to herbivore / defense response to insect / peptide receptor activity / jasmonic acid biosynthetic process / cellular response to peptide / plasmodesma / peptide binding / response to molecule of bacterial origin / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Wan, L.H. / Hu, Y.X. / Wu, H.M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature Plants / Year: 2024 Title: Mechanistic study of SCOOPs recognition by MIK2-BAK1 complex reveals the role of N-glycans in plant ligand-receptor-coreceptor complex formation Authors: Hu, Y.X. / Wu, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8web.cif.gz | 283.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8web.ent.gz | 226.9 KB | Display | PDB format |
PDBx/mmJSON format | 8web.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8web_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 8web_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 8web_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 8web_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/8web ftp://data.pdbj.org/pub/pdb/validation_reports/we/8web | HTTPS FTP |
-Related structure data
Related structure data | 8wecC 8wedC 8weeC 8wefC 8wegC 8wehC 8weiC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 78853.930 Da / Num. of mol.: 1 / Mutation: L137E/D164K/S564F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MIK2, At4g08850, T32A17.160 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q8VZG8, non-specific serine/threonine protein kinase | ||||||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.77 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 7.4 Details: 0.2 M Sodium acetate, 0.1 M Tris pH 7.4 and 18% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 81379 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 1 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique obs: 6952 / CC1/2: 0.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.13 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→35.13 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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