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Yorodumi- PDB-3mh7: HtrA proteases are activated by a conserved mechanism that can be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mh7 | ||||||
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Title | HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues | ||||||
Components |
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Keywords | HYDROLASE / DegP / HtrA / protease / outer membrane protein | ||||||
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 / SAD / Resolution: 2.961 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 | 3mh7.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mh7.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/3mh7 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/3mh7 | 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: 48582.594 Da / Num. of mol.: 1 / Mutation: S210A 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: Protein/peptide | Mass: 443.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: this peptide apparently picked up during protein purification. Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: DegP / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) Sequence details | THE DEPOSITORS COULD NOT DETERMINE THE SEQUENCE FOR CHAIN B, C AND COULD NOT PROVE WHETHER CHIAN B ...THE DEPOSITORS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.32 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 8.5 Details: PEG 550 MME, NaCl, pH 8.5, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.961→30 Å / Num. obs: 15145 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.961→3.19 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.579 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.961→29.321 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.828 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.861 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.98 Å2 / Biso mean: 75.679 Å2 / Biso min: 33.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.961→29.321 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: 5 / % reflection obs: 100 %
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