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- PDB-6g3w: Crystal structure of the BIR3 - SERK2 complex from Arabidopsis th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6g3w | |||||||||
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Title | Crystal structure of the BIR3 - SERK2 complex from Arabidopsis thaliana. | |||||||||
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![]() | PROTEIN BINDING / leucine rich repeat receptor / membrane receptor / pseudokinase / ectodomain / receptor complex / negative regulator | |||||||||
Function / homology | ![]() microsporogenesis / pollen maturation / brassinosteroid mediated signaling pathway / receptor serine/threonine kinase binding / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein phosphorylation / protein serine kinase activity / signaling receptor binding ...microsporogenesis / pollen maturation / brassinosteroid mediated signaling pathway / receptor serine/threonine kinase binding / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein phosphorylation / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / lipid binding / ATP binding / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hothorn, M. / Hohmann, U. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The SERK3 elongated allele defines a role for BIR ectodomains in brassinosteroid signalling. Authors: Hohmann, U. / Nicolet, J. / Moretti, A. / Hothorn, L.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 | ![]() | 305.8 KB | Display | ![]() |
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PDB format | ![]() | 248.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fg7C ![]() 6fg8SC ![]() 4z61S 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 23975.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9XIC7, non-specific serine/threonine protein kinase #2: Protein | Mass: 21127.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 8 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 146 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-PEG / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% (w/v) PEG 3,350, 0.2 M MgCl_2 x 6H_2O, 0.1 M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000027 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.41 Å / Num. obs: 42439 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.115 / Rsym value: 0.111 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 13 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6697 / CC1/2: 0.71 / Rrim(I) all: 1.67 / Rsym value: 1.604 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6fg8, 4z61 Resolution: 2.2→49.41 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 16.233 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.214 / 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: 61.234 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→49.41 Å
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Refine LS restraints |
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