+Open data
-Basic information
Entry | Database: PDB / ID: 4j0m | |||||||||
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Title | Crystal structure of BRL1 (LRR) in complex with brassinolide | |||||||||
Components | Serine/threonine-protein kinase BRI1-like 1 | |||||||||
Keywords | TRANSFERASE / leucine-rich repeat / receptor | |||||||||
Function / homology | Function and homology information steroid binding / hormone-mediated signaling pathway / membrane => GO:0016020 / non-specific serine/threonine protein kinase / 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: 2.5 Å | |||||||||
Authors | Chai, J. / She, J. / Han, Z. / Zhou, B. | |||||||||
Citation | Journal: Protein Cell / Year: 2013 Title: Structural basis for differential recognition of brassinolide by its receptors Authors: She, J. / Han, Z. / Zhou, B. / Chai, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j0m.cif.gz | 301.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j0m.ent.gz | 242.7 KB | Display | PDB format |
PDBx/mmJSON format | 4j0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j0m_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 4j0m_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 4j0m_validation.xml.gz | 60.7 KB | Display | |
Data in CIF | 4j0m_validation.cif.gz | 83.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/4j0m ftp://data.pdbj.org/pub/pdb/validation_reports/j0/4j0m | HTTPS FTP |
-Related structure data
Related structure data | 3rgzS S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 79634.875 Da / Num. of mol.: 2 / Fragment: UNP residues 25-758 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BRL1, At1g55610, F20N2.4 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9ZWC8, non-specific serine/threonine protein kinase |
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-Sugars , 3 types, 13 molecules
#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: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 413 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 3.63 Å3/Da / Density % sol: 66.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.2M ammonium citrate dibasic, 20% (w/v) polyethylene glycol (PEG) 3350, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 25, 2012 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 79466 / Num. obs: 75248 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 31.89 Å2 |
Reflection shell | Resolution: 2.5→2.54 Å / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RGZ Resolution: 2.5→29.829 Å / Occupancy max: 1 / Occupancy min: 0.84 / FOM work R set: 0.8144 / SU ML: 0.32 / σ(F): 0 / Phase error: 25.48 / 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: 100.89 Å2 / Biso mean: 25.8164 Å2 / Biso min: 7.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.829 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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