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Yorodumi- PDB-2r3y: Crystal structure of the DegS protease in complex with the YWF ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r3y | ||||||
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Title | Crystal structure of the DegS protease in complex with the YWF activating peptide | ||||||
Components |
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Keywords | hydrolase/hydrolase activator / reversible activation of a protease / catalytic triad / Hydrolase / Periplasm / Serine protease / hydrolase-hydrolase activator COMPLEX | ||||||
Function / homology | Function and homology information peptidase Do / cellular response to misfolded protein / serine-type peptidase activity / outer membrane-bounded periplasmic space / peptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Clausen, T. / Hasselblatt, H. | ||||||
Citation | Journal: Genes Dev. / Year: 2007 Title: Regulation of the sigmaE stress response by DegS: how the PDZ domain keeps the protease inactive in the resting state and allows integration of different OMP-derived stress signals upon folding stress. Authors: Hasselblatt, H. / Kurzbauer, R. / Wilken, C. / Krojer, T. / Sawa, J. / Kurt, J. / Kirk, R. / Hasenbein, S. / Ehrmann, M. / Clausen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r3y.cif.gz | 169.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r3y.ent.gz | 134.4 KB | Display | PDB format |
PDBx/mmJSON format | 2r3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/2r3y ftp://data.pdbj.org/pub/pdb/validation_reports/r3/2r3y | HTTPS FTP |
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-Related structure data
Related structure data | 2r3uC 1sozS 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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1 |
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Unit cell |
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Details | One homotrimer of DegS was observed in the asymmetric unit and should represent its physiological state. |
-Components
#1: Protein | Mass: 33243.664 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: degS, hhoB, htrH / Plasmid: pET15-b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0AEE3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein/peptide | Mass: 1283.455 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: The YWF peptide mimics the C-terminus of Outer Membrane Proteins. #3: 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: 2.91 Å3/Da / Density % sol: 57.77 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: The YWF (100 microM) was added to DegS and incubated 30 minutes before setting up the co-crystallization trials. Crystals of the complex were grown in sitting drops at 19 C by mixing 4 ...Details: The YWF (100 microM) was added to DegS and incubated 30 minutes before setting up the co-crystallization trials. Crystals of the complex were grown in sitting drops at 19 C by mixing 4 microL of DegS/YWF with 2 microL of a crystallization solution containing 0.1 M HEPES (pH 7.5), 6% PEG 6000, 9% MPD and 10 mM MgCl2. Crystal trials were set up in cryschem plates with a reservoir volume of 400 microL. , VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 30, 2006 / Details: mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 39228 / Num. obs: 39228 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.047 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / Num. unique all: 3644 / Rsym value: 0.33 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1soz Resolution: 2.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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