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Yorodumi- PDB-3mh6: HtrA proteases are activated by a conserved mechanism that can be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mh6 | ||||||
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Title | HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues | ||||||
Components | Protease doPeptidase Do | ||||||
Keywords | HYDROLASE / DegP / HtrA / protease | ||||||
Function / homology | Function and homology information peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / outer membrane-bounded periplasmic space / peptidase activity / response to heat / response to oxidative stress ...peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / outer membrane-bounded periplasmic space / peptidase activity / response to heat / response to oxidative stress / periplasmic space / 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: 3.6 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 | 3mh6.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mh6.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/3mh6 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/3mh6 | HTTPS FTP |
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-Related structure data
Related structure data | 3mh4C 3mh5C 3mh7C 3cs0S 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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Unit cell |
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-Components
#1: Protein | Mass: 47942.070 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-DFP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.05 % |
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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: SLS / Beamline: X06SA |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.6→29.24 Å / Num. all: 9340 / Num. obs: 9340 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 77.8 Å2 / Rmerge(I) obs: 0.243 / Rsym value: 0.243 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3.6→3.79 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1318 / Rsym value: 0.787 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CS0 Resolution: 3.6→28.703 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.66 / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 37.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.836 Å2 / ksol: 0.237 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 287.98 Å2 / Biso mean: 129.65 Å2 / Biso min: 68.63 Å2
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Refinement step | Cycle: LAST / Resolution: 3.6→28.703 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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