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Yorodumi- PDB-2jol: Average NMR structure of the catalytic domain of guanine nucleoti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jol | |||||||||
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Title | Average NMR structure of the catalytic domain of guanine nucleotide exchange factor BopE from Burkholderia pseudomallei | |||||||||
Components | Putative G-nucleotide exchange factor | |||||||||
Keywords | CELL INVASION / SIGNALING PROTEIN / Guanine nucleotide exchange factor / Burkholderia pseudomallei / Type III secretion / SopE / SopE2 | |||||||||
Function / homology | Function and homology information GTPase activator activity / guanyl-nucleotide exchange factor activity / actin cytoskeleton organization / extracellular region Similarity search - Function | |||||||||
Biological species | Burkholderia pseudomallei (bacteria) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Model details | Average of solution structure of BopE | |||||||||
Model type details | minimized average | |||||||||
Authors | Wu, H. / Upadhyay, A. / Williams, C. / Galyov, E.E. / van den Elsen, J.M.H. / Bagby, S. | |||||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: The guanine-nucleotide-exchange factor BopE from Burkholderia pseudomallei adopts a compact version of the Salmonella SopE/SopE2 fold and undergoes a closed-to-open conformational change upon ...Title: The guanine-nucleotide-exchange factor BopE from Burkholderia pseudomallei adopts a compact version of the Salmonella SopE/SopE2 fold and undergoes a closed-to-open conformational change upon interaction with Cdc42 Authors: Upadhyay, A. / Wu, H.L. / Williams, C. / Field, T. / Galyov, E.E. / van den Elsen, J.M. / Bagby, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jol.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jol.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/2jol ftp://data.pdbj.org/pub/pdb/validation_reports/jo/2jol | HTTPS FTP |
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-Related structure data
Related structure data | 2jokC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20136.344 Da / Num. of mol.: 1 / Fragment: residues 78-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: bopE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q63K41 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: Average of solution structure of BopE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8 mM protein, 20 mM potassium phosphate, 50 mM sodium chloride, 10 mM DTT, 1 mM benzamidine, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 5.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 1 |