+Open data
-Basic information
Entry | Database: PDB / ID: 4q5j | ||||||
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Title | Crystal structure of SeMet derivative BRI1 in complex with BKI1 | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / kinase domain / ATP binding / Phosphorylation / SeMet labelled / Membrane / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of brassinosteroid biosynthetic process / 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 ...negative regulation of brassinosteroid biosynthetic process / 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 / protein kinase inhibitor activity / steroid binding / transmembrane receptor protein tyrosine kinase activity / lipid metabolic process / 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 / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.772 Å | ||||||
Authors | Wang, J. / Wang, J. / Chen, L. / Wu, J.W. / Wang, Z.X. | ||||||
Citation | Journal: Cell Res. / Year: 2014 Title: Structural insights into the negative regulation of BRI1 signaling by BRI1-interacting protein BKI1. Authors: Wang, J. / Jiang, J. / Wang, J. / Chen, L. / Fan, S.L. / Wu, J.W. / Wang, X. / Wang, Z.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q5j.cif.gz | 261.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q5j.ent.gz | 213.4 KB | Display | PDB format |
PDBx/mmJSON format | 4q5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/4q5j ftp://data.pdbj.org/pub/pdb/validation_reports/q5/4q5j | HTTPS FTP |
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-Related structure data
Related structure data | 4oh4SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38972.102 Da / Num. of mol.: 2 / Fragment: kinase domain, UNP residues 863-1180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g39400, BRI1, F23K16.30 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase #2: Protein/peptide | Mass: 2281.564 Da / Num. of mol.: 2 / Fragment: C-terminal peptide, UNP residues 306-325 / Source method: obtained synthetically Details: This sequence occurs naturally in Arabidopsis thaliana. Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FMZ0 #3: Chemical | #4: 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: 2.35 Å3/Da / Density % sol: 47.73 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2M ithium Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→50 Å / Num. all: 19482 / Num. obs: 19437 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 71.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.77→2.87 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1906 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OH4 Resolution: 2.772→38.409 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 36.04 / Stereochemistry target values: ML Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.772→38.409 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: 7
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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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