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Open data
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Basic information
Entry | Database: PDB / ID: 4e6x | ||||||
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Title | ClbP in complex boron-based inhibitor | ||||||
![]() | ClbP peptidase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / alpha/beta / ![]() ![]() | ||||||
Function / homology | ![]() antibiotic catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cougnoux, A. / Delmas, J. / Bonnet, R. | ||||||
![]() | ![]() Title: The NRP peptidase ClbP as a target for the inhibition of genotoxicity, cell proliferation and tumorogenesis mediated by pks-harboring bacteria Authors: Cougnoux, A. / Delmas, J. / Dalmasso, G. / Romagnoli, C. / Cuevas-Ramos, G. / Oswald, E. / Prati, F. / Bonnet, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.1 KB | Display | ![]() |
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PDB format | ![]() | 149.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4e6wC ![]() 3o3vS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36871.082 Da / Num. of mol.: 3 / Fragment: UNP residues 41-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8FGC8, UniProt: A0A0H2V8D3*PLUS, ![]() #2: Chemical | ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.24→52.6 Å / Num. obs: 40985 / % possible obs: 79 % |
Reflection shell | Resolution: 2.24→2.36 Å / % possible all: 80.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3O3V Resolution: 2.24→52.55 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.128 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→52.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.298 Å / Total num. of bins used: 20
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