+Open data
-Basic information
Entry | Database: PDB / ID: 4e6w | ||||||
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Title | ClbP in complex with 3-aminophenyl boronic acid | ||||||
Components | ClbP peptidase | ||||||
Keywords | HYDROLASE / alpha/beta / disulfide bridge / peptidase | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / membrane => GO:0016020 / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Cougnoux, A. / Delmas, J. / Bonnet, R. | ||||||
Citation | Journal: To be Published 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. / Parti, F. / Bonnet, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e6w.cif.gz | 207.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e6w.ent.gz | 165.5 KB | Display | PDB format |
PDBx/mmJSON format | 4e6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/4e6w ftp://data.pdbj.org/pub/pdb/validation_reports/e6/4e6w | HTTPS FTP |
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-Related structure data
Related structure data | 4e6xC 3o3vS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36800.004 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O6 / Gene: c2452 / Plasmid: pET9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8FGC8, UniProt: A0A0H2V8D3*PLUS, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: 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: 2.58 Å3/Da / Density % sol: 52.31 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å |
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: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→52.2 Å / Num. obs: 54118 / % possible obs: 99.7 % |
Reflection shell | Resolution: 2.19→2.31 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3O3V Resolution: 2.19→52.2 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.207 / 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: 27.251 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→52.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.192→2.249 Å / Total num. of bins used: 20
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