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Yorodumi- PDB-2ehb: The structure of the C-terminal domain of the protein kinase AtSO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ehb | ||||||
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Title | The structure of the C-terminal domain of the protein kinase AtSOS2 bound to the calcium sensor AtSOS3 | ||||||
Components |
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Keywords | SIGNALLING PROTEIN/Transferase / protein complex / Ca(II) ions bound to SOS3 (EF-hands 1 and 4) / SOS2 FISL motif / SOS2 phosphatase binding domain (PPI) / SIGNALLING PROTEIN-Transferase COMPLEX | ||||||
Function / homology | Function and homology information hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / plant-type vacuole membrane / calcineurin complex / intracellular potassium ion homeostasis / mitotic G2 DNA damage checkpoint signaling / detection of calcium ion / response to salt stress / calcium-mediated signaling / kinase binding ...hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / plant-type vacuole membrane / calcineurin complex / intracellular potassium ion homeostasis / mitotic G2 DNA damage checkpoint signaling / detection of calcium ion / response to salt stress / calcium-mediated signaling / kinase binding / site of double-strand break / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sanchez-Barrena, M.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: The structure of the C-terminal domain of the protein kinase AtSOS2 bound to the calcium sensor AtSOS3 Authors: Sanchez-Barrena, M.J. / Fujii, H. / Angulo, I. / Martinez-Ripoll, M. / Zhu, J.K. / Albert, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ehb.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ehb.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ehb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ehb_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 2ehb_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 2ehb_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 2ehb_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/2ehb ftp://data.pdbj.org/pub/pdb/validation_reports/eh/2ehb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24045.750 Da / Num. of mol.: 1 / Fragment: residues in database 1-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOS3 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3) / References: UniProt: O81223 | ||
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#2: Protein | Mass: 16368.982 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 304-446) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOS2 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3) References: UniProt: Q9LDI3, non-specific serine/threonine protein kinase | ||
#3: Chemical | #4: 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: 2.22 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: drops: 10mg/ml SOS3:C-SOS2, reservoir solution: 20%(w/v) PEG4000, 0.1M Tris-HCl pH 7.5, 0.2M Lithium Sulfate, 3%(v/v) Ethylene Glycol; 1M Guanidine HCl in a ratio of 1:1:0.5, VAPOR ...Details: drops: 10mg/ml SOS3:C-SOS2, reservoir solution: 20%(w/v) PEG4000, 0.1M Tris-HCl pH 7.5, 0.2M Lithium Sulfate, 3%(v/v) Ethylene Glycol; 1M Guanidine HCl in a ratio of 1:1:0.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2006 Details: The main optical elements are a liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror, the latter which is bent to approximate to a toroidal curvature. |
Radiation | Monochromator: There is a high resolution Si(311) cut and a lower resolution Si(111) cut Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→70.9 Å / Num. all: 25141 / Num. obs: 25141 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.35 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Structure of SOS3 Resolution: 2.1→70.89 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.57 / SU ML: 0.17 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.242 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.969 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→70.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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