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- PDB-5ixq: Crystal structure of the Arabidopsis receptor kinase HAESA LRR ec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ixq | |||||||||
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Title | Crystal structure of the Arabidopsis receptor kinase HAESA LRR ectdomain in complex with the peptide hormone IDA. | |||||||||
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Function / homology | ![]() lateral root morphogenesis / regulation of cell diameter / leaf abscission / floral organ abscission / response to ethylene / pectin catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Santiago, J. / Hothorn, M. | |||||||||
![]() | ![]() Title: Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission. Authors: Santiago, J. / Brandt, B. / Wildhagen, M. / Hohmann, U. / Hothorn, L.A. / Butenko, M.A. / Hothorn, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.3 KB | Display | ![]() |
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PDB format | ![]() | 201.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ixoSC ![]() 5ixtC ![]() 5iyvC ![]() 5iyxC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 67216.195 Da / Num. of mol.: 1 / Fragment: ectodomain, residues 20-620 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P47735, ![]() ![]() |
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#2: Protein/peptide | Mass: 1319.489 Da / Num. of mol.: 1 / Fragment: UNP residues 58-69 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-Sugars , 3 types, 7 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ![]() Source method: isolated from a genetically manipulated source #5: Sugar | ![]() |
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-Non-polymers , 3 types, 42 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-EDO / | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.15 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 19% PEG 3350, 0.2 M MgCl2, 0.1 M citric acid pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.86→128.42 Å / Num. obs: 61813 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 20.3 % / Biso Wilson estimate: 80 Å2 / CC1/2: 1 / Rsym value: 0.055 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.86→1.97 Å / Redundancy: 19.1 % / Mean I/σ(I) obs: 2 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5IXO Resolution: 1.86→128.42 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 6.94 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.083 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→128.42 Å
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Refine LS restraints |
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