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Yorodumi- PDB-3mh5: HtrA proteases are activated by a conserved mechanism that can be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mh5 | ||||||
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Title | HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues | ||||||
Components | Protease do | ||||||
Keywords | HYDROLASE / DegP / HtrA / protease | ||||||
Function / homology | Function and homology information peptidase Do / programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / response to heat / outer membrane-bounded periplasmic space ...peptidase Do / programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / response to heat / outer membrane-bounded periplasmic space / response to oxidative stress / periplasmic space / positive regulation of apoptotic process / 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: 3 Å | ||||||
Authors | Krojer, T. / Sawa, J. / Huber, R. / Clausen, T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: HtrA proteases have a conserved activation mechanism that can be triggered by distinct molecular cues Authors: Krojer, T. / Sawa, J. / Huber, R. / Clausen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mh5.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mh5.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mh5_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 3mh5_full_validation.pdf.gz | 469.5 KB | Display | |
Data in XML | 3mh5_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3mh5_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/3mh5 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/3mh5 | HTTPS FTP |
-Related structure data
Related structure data | 3mh4C 3mh6C 3mh7C 1ky9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47942.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: DegP / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) References: UniProt: P0C0V0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | #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: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. all: 20353 / Num. obs: 20353 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 94.6 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 3→3.07 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1329 / Rsym value: 0.435 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KY9 Resolution: 3→20 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: 3→20 Å
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