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- PDB-5lpy: Crystal structure of the BRI1 kinase domain (865-1160) in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lpy | |||||||||
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Title | Crystal structure of the BRI1 kinase domain (865-1160) in complex with ATP from Arabidopsis thaliana | |||||||||
![]() | Protein BRASSINOSTEROID INSENSITIVE 1 | |||||||||
![]() | TRANSFERASE / brassinosteroid receptor / kinase domain / dual-specificify kinase / membrane receptor kinase / plasma membrane | |||||||||
Function / homology | ![]() detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / microtubule bundle formation ...detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / microtubule bundle formation / response to UV-B / steroid binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / non-specific serine/threonine protein kinase / endosome membrane / protein kinase activity / endosome / protein heterodimerization activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bojar, D. / Martinez, J. / Hothorn, M. | |||||||||
![]() | ![]() Title: Crystal structure of the BRI1 kinase domain (865-1160) in complex with ATP from Arabidopsis thaliana Authors: Bojar, D. / Martinez, J. / Hothorn, M. #1: ![]() Title: Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation. Authors: Bojar, D. / Martinez, J. / Santiago, J. / Rybin, V. / Bayliss, R. / 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 | ![]() | 130.1 KB | Display | ![]() |
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PDB format | ![]() | 100.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.5 KB | Display | ![]() |
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Full document | ![]() | 761.9 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lpbC ![]() 5lpwC ![]() 5lpzC ![]() 3uimS 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
#1: Protein | Mass: 33442.203 Da / Num. of mol.: 1 / Mutation: T872A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ATP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28% PEG 20K/MME 550 morpheus mix, 0.12 M eth glycol mix, 0.1 M Hepes pH 7.5 soaked with 30 mM ATP in xtal condition (around 3 min) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.67 Å / Num. obs: 17194 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 71.46 Å2 / CC1/2: 1 / Rsym value: 0.043 / Net I/σ(I): 36.77 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 2.49 / CC1/2: 0.767 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UIM Resolution: 2.3→44.67 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.67 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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