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Open data
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Basic information
Entry | Database: PDB / ID: 6jjo | ||||||
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Title | Crystal structure of the DegP dodecamer with a modulator | ||||||
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![]() | HYDROLASE / Protease | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, H. / Choi, Y. / Lee, H.H. / Kim, S. | ||||||
![]() | ![]() Title: Over-activation of a nonessential bacterial protease DegP as an antibiotic strategy Authors: Cho, H. / Choi, Y. / Min, K. / Son, J.B. / Park, H. / Lee, H.H. / Kim, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 429.1 KB | Display | ![]() |
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PDB format | ![]() | 346.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.6 KB | Display | ![]() |
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Full document | ![]() | 506.1 KB | Display | |
Data in XML | ![]() | 45.5 KB | Display | |
Data in CIF | ![]() | 68.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jjkC ![]() 6jjlC ![]() 3otpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49155.473 Da / Num. of mol.: 6 / Mutation: S210A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 683.863 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 11% PEG3350 and 0.1 M tacsimate pH 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.2→50 Å / Num. obs: 24531 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 151.78 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.045 / Rrim(I) all: 0.121 / Χ2: 1.944 / Net I/σ(I): 9.1 / Num. measured all: 176600 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3OTP Resolution: 4.157→35.61 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 325.25 Å2 / Biso mean: 174.9717 Å2 / Biso min: 94.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.157→35.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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