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Yorodumi- PDB-5lpz: Crystal structure of the BRI1 kinase domain (865-1196) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lpz | |||||||||
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Title | Crystal structure of the BRI1 kinase domain (865-1196) in complex with ADP from Arabidopsis thaliana | |||||||||
Components | Protein BRASSINOSTEROID INSENSITIVE 1 | |||||||||
Keywords | TRANSFERASE / brassinosteroid receptor / kinase domain / dual-specificify kinase / membrane receptor kinase / plasma membrane | |||||||||
Function / homology | Function and homology information 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 / endosome membrane / non-specific serine/threonine protein kinase / endosome / protein kinase activity / 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 | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | |||||||||
Authors | Bojar, D. / Martinez, J. / Hothorn, M. | |||||||||
Citation | Journal: Plant J. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lpz.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lpz.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 5lpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/5lpz ftp://data.pdbj.org/pub/pdb/validation_reports/lp/5lpz | HTTPS FTP |
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-Related structure data
Related structure data | 5lpbC 5lpwC 3uimS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37161.430 Da / Num. of mol.: 1 / Fragment: UNP residues 865-1196 / Mutation: T872A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BRI1, At4g39400, F23K16.30 / Plasmid: pMH-HT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 37.5% MPD/PEG 1000/PEG 3350 morpheus mix, 0.1 M amino acids mix, 0.1 M MOPS/Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91838 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91838 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→19.47 Å / Num. obs: 14064 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 20.02 % / Biso Wilson estimate: 67.34 Å2 / CC1/2: 1 / Rsym value: 0.097 / Net I/σ(I): 22.43 |
Reflection shell | Resolution: 2.48→2.62 Å / Redundancy: 18.66 % / Mean I/σ(I) obs: 2.63 / CC1/2: 0.794 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UIM Resolution: 2.48→19.47 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.56 / Phase error: 30.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→19.47 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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