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Yorodumi- PDB-1soz: Crystal Structure of DegS protease in complex with an activating ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1soz | ||||||
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Title | Crystal Structure of DegS protease in complex with an activating peptide | ||||||
Components |
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Keywords | HYDROLASE / stress response / protein quality control / PDZ / UPR / HtrA | ||||||
Function / homology | Function and homology information : / peptidase Do / cellular response to misfolded protein / serine-type peptidase activity / outer membrane-bounded periplasmic space / peptidase activity / membrane => GO:0016020 / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wilken, C. / Kitzing, K. / Kurzbauer, R. / Ehrmann, M. / Clausen, T. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 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: Journal: Cell(Cambridge,Mass.) / Year: 2003 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1soz.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1soz.ent.gz | 131.6 KB | Display | PDB format |
PDBx/mmJSON format | 1soz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/1soz ftp://data.pdbj.org/pub/pdb/validation_reports/so/1soz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Escherichia coli (E. coli) / Gene: DEGS, HHOB, HTRH, B3235, Z4594, ECS4108 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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