+Open data
-Basic information
Entry | Database: PDB / ID: 4i93 | ||||||
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Title | Structure of the BSK8 kinase domain (SeMet labeled) | ||||||
Components | Probable serine/threonine-protein kinase At5g41260 | ||||||
Keywords | TRANSFERASE / Protein kinase / Pseudo kinase / CFG / Alanine Gatekeeper / Transferase Brassinosteroid-signaling / SeMet Derivative | ||||||
Function / homology | Function and homology information brassinosteroid mediated signaling pathway / plastid / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Gruetter, C. / Rauh, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structural Characterization of the RLCK Family Member BSK8: A Pseudokinase with an Unprecedented Architecture Authors: Grutter, C. / Sreeramulu, S. / Sessa, G. / Rauh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i93.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i93.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 4i93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/4i93 ftp://data.pdbj.org/pub/pdb/validation_reports/i9/4i93 | HTTPS FTP |
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-Related 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: 34810.238 Da / Num. of mol.: 2 / Fragment: BSK8 Kinase Domain, UNP residues 40-328 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g41260, K1O13.5 / Plasmid: pTriEx-2-based multi-host vector pOPINE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9FHD7, non-specific serine/threonine protein kinase #2: 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: 1.86 Å3/Da / Density % sol: 33.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15-25%(w/v) PEG3350, 200mM KSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 29, 2008 / Details: Si(111) monochromator, Dynamically bendable mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) monochromator, Dynamically bendable mirror Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Number: 334535 / Rmerge(I) obs: 0.029 / D res high: 1.5 Å / Num. obs: 151021 / % possible obs: 93.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.5→35 Å / Num. all: 81558 / Num. obs: 79966 / % possible obs: 98.05 % / Observed criterion σ(I): -3 / Redundancy: 4.23 % / Biso Wilson estimate: 21.682 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→33.39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2151 / WRfactor Rwork: 0.1918 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8641 / SU B: 1.436 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0803 / SU Rfree: 0.0797 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.61 Å2 / Biso mean: 18.394 Å2 / Biso min: 6.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→33.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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