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Yorodumi- PDB-1r9k: Representative solution structure of the catalytic domain of SopE2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r9k | ||||||
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Title | Representative solution structure of the catalytic domain of SopE2 | ||||||
Components | TypeIII-secreted protein effector: invasion-associated protein | ||||||
Keywords | CELL INVASION / Salmonella / invasion / type III / GEF / SopE | ||||||
Function / homology | Function and homology information GTPase activator activity / guanyl-nucleotide exchange factor activity / actin cytoskeleton organization / extracellular region Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Williams, C. / Galyov, E.E. / Bagby, S. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Solution Structure, Backbone Dynamics, and Interaction with Cdc42 of Salmonella Guanine Nucleotide Exchange Factor SopE2(,). Authors: Williams, C. / Galyov, E.E. / Bagby, S. #1: Journal: To be Published / Year: 2003 Title: Biochemical and structural analysis of Salmonella and Burkholderia virulence proteins Authors: Williams, C. #2: Journal: J.BIOMOL.NMR / Year: 2003 Title: Assignment of the 1H,13C and 15N resonances of the catalytic domain of guanine nucelotide exchange factor SopE2 from Salmonella dublin Authors: Williams, C. / Galyov, E.E. / Bagby, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r9k.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r9k.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/1r9k ftp://data.pdbj.org/pub/pdb/validation_reports/r9/1r9k | HTTPS FTP |
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-Related structure data
Related structure data | 1r6eC 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: 18585.338 Da / Num. of mol.: 1 / Fragment: SopE2 GEF domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: sopE2 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KIZ2, UniProt: Q7CQD4*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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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 Details: he structures are based on a total of 3065 restraints, 2682 are NOE-derived distance constraints, 249 dihedral angle restraints,134 distance restraints from hydrogen bonds. | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 1 |