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Yorodumi- PDB-5xkj: Crystal structure of plant receptor ERL1-TMM in complexe with EPF2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xkj | |||||||||
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Title | Crystal structure of plant receptor ERL1-TMM in complexe with EPF2 | |||||||||
Components |
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Keywords | TRANSFERASE/MEMBRANE PROTEIN/HORMONE / stomata development ER / family TMM / peptide hormone EPFs / TRANSFERASE-MEMBRANE PROTEIN-HORMONE complex | |||||||||
Function / homology | Function and homology information plant epidermis morphogenesis / negative regulation of stomatal complex development / regulation of antifungal innate immune response / guard cell differentiation / trichome morphogenesis / stomatal complex morphogenesis / stomatal complex formation / stomatal complex patterning / cellular response to abscisic acid stimulus / stomatal complex development ...plant epidermis morphogenesis / negative regulation of stomatal complex development / regulation of antifungal innate immune response / guard cell differentiation / trichome morphogenesis / stomatal complex morphogenesis / stomatal complex formation / stomatal complex patterning / cellular response to abscisic acid stimulus / stomatal complex development / plant ovule development / embryo sac development / asymmetric cell division / response to abscisic acid / receptor serine/threonine kinase binding / defense response to fungus / peptide binding / non-specific serine/threonine protein kinase / phosphorylation / signaling receptor binding / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / protein kinase binding / extracellular region / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.475 Å | |||||||||
Authors | Chai, J. / Lin, G. | |||||||||
Funding support | China, 2items
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Citation | Journal: Genes Dev. / Year: 2017 Title: A receptor-like protein acts as a specificity switch for the regulation of stomatal development. Authors: Lin, G. / Zhang, L. / Han, Z. / Yang, X. / Liu, W. / Li, E. / Chang, J. / Qi, Y. / Shpak, E.D. / Chai, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xkj.cif.gz | 681.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xkj.ent.gz | 562.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/5xkj ftp://data.pdbj.org/pub/pdb/validation_reports/xk/5xkj | HTTPS FTP |
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-Related structure data
Related structure data | 5xjoC 5xjxC 5xknC 4mn8S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47465.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TMM, RLP17, At1g80080, F18B13.16 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9SSD1 #2: Protein | Mass: 5669.548 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EPF2, At1g34245, F23M19 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8LC53 #3: Protein | Mass: 60419.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ERL1, At5g62230, MMI9.14 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: C0LGW6, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 mM Ammonium citrate tribasic pH 7.0, 10% Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Oct 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→50 Å / Num. obs: 29462 / % possible obs: 93.8 % / Redundancy: 3 % / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.4751→3.5993 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MN8 Resolution: 3.475→46.186 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 31.36 / 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: 3.475→46.186 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: -39.8 Å / Origin y: 3.0775 Å / Origin z: 94.4339 Å
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Refinement TLS group | Selection details: all |