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- PDB-1soz: Crystal Structure of DegS protease in complex with an activating ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1soz | ||||||
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Title | Crystal Structure of DegS protease in complex with an activating peptide | ||||||
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![]() | HYDROLASE / stress response / protein quality control / PDZ / UPR / HtrA | ||||||
Function / homology | ![]() : / peptidase Do / cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / serine-type peptidase activity / peptidase activity / outer membrane-bounded periplasmic space / membrane => GO:0016020 / serine-type endopeptidase activity / proteolysis ...: / peptidase Do / cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / serine-type peptidase activity / peptidase activity / outer membrane-bounded periplasmic space / membrane => GO:0016020 / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilken, C. / Kitzing, K. / Kurzbauer, R. / Ehrmann, M. / Clausen, T. | ||||||
![]() | ![]() Title: Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease Authors: Wilken, C. / Kitzing, K. / Kurzbauer, R. / Ehrmann, M. / Clausen, T. #1: ![]() Title: OMP peptide signals initiate the envelope-stress response by activating DegS protease via relief of inhibition mediated by its PDZ domain Authors: Walsh, N.P. / Alba, B.M. / Bose, B. / Gross, C.A. / Sauer, R.T. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.7 KB | Display | ![]() |
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PDB format | ![]() | 131.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.3 KB | Display | ![]() |
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Full document | ![]() | 520.7 KB | Display | |
Data in XML | ![]() | 37.9 KB | Display | |
Data in CIF | ![]() | 52 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33243.664 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P31137, UniProt: P0AEE3*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein/peptide | Mass: 1225.374 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.35 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 6000, MPD, HEPES, magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. all: 42509 / Num. obs: 42042 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: DegS, uncomplexed Resolution: 2.4→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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