+Open data
-Basic information
Entry | Database: PDB / ID: 7xdx | ||||||
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Title | Crystal structure of a receptor like kinase from Arabidopsis | ||||||
Components | Receptor-like protein kinase FERONIA | ||||||
Keywords | RIBOSOMAL PROTEIN / receptor-like kinase | ||||||
Function / homology | Function and homology information pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / response to brassinosteroid / response to ethylene / brassinosteroid mediated signaling pathway / ethylene-activated signaling pathway / stomatal movement / root development / plasmodesma ...pollen tube reception / filiform apparatus / negative regulation of abscisic acid-activated signaling pathway / response to brassinosteroid / response to ethylene / brassinosteroid mediated signaling pathway / ethylene-activated signaling pathway / stomatal movement / root development / plasmodesma / abscisic acid-activated signaling pathway / defense response to fungus / transmembrane receptor protein tyrosine kinase activity / post-embryonic development / circadian regulation of gene expression / negative regulation of cell growth / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / 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: 2.23 Å | ||||||
Authors | Kong, Y.Q. / Ming, Z.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Plant Commun. / Year: 2023 Title: Structural and biochemical basis of Arabidopsis FERONIA receptor kinase-mediated early signaling initiation. Authors: Kong, Y. / Chen, J. / Jiang, L. / Chen, H. / Shen, Y. / Wang, L. / Yan, Y. / Zhou, H. / Zheng, H. / Yu, F. / Ming, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xdx.cif.gz | 245.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xdx.ent.gz | 193.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/7xdx ftp://data.pdbj.org/pub/pdb/validation_reports/xd/7xdx | HTTPS FTP |
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-Related structure data
Related structure data | 7xdvC 7xdwC 7xdyC 2qkwS S: Starting model for refinement 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 521 - 815 / Label seq-ID: 18 - 312
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-Components
#1: Protein | Mass: 35495.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FER, AAK1, SIR, SRN, At3g51550, F26O13.190 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9SCZ4, non-specific serine/threonine protein kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.23 Å3/Da / Density % sol: 44.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.0, 30% v/v Polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→82.95 Å / Num. obs: 30350 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.23→2.29 Å / Num. unique obs: 28857 / CC1/2: 0.982 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QKW Resolution: 2.23→61.568 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.29 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 173.77 Å2 / Biso mean: 38.8881 Å2 / Biso min: 8.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→61.568 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 13.5549 Å / Origin y: 5.2665 Å / Origin z: 16.6325 Å
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Refinement TLS group |
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