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- PDB-5eph: Crystal structure of extended-spectrum beta-lactamase BEL-1 in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5eph | |||||||||
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Title | Crystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Imipenem | |||||||||
![]() | Beta-lactamase | |||||||||
![]() | HYDROLASE/ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex / extended-spectrum beta-lactamase / Pseudomonas aeruginosa | |||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pozzi, C. / Benvenuti, M. / De Luca, F. / Docquier, J.D. / Mangani, S. | |||||||||
![]() | ![]() Title: Crystal Structure of the Pseudomonas aeruginosa BEL-1 Extended-Spectrum beta-Lactamase and Its Complexes with Moxalactam and Imipenem. Authors: Pozzi, C. / De Luca, F. / Benvenuti, M. / Poirel, L. / Nordmann, P. / Rossolini, G.M. / Mangani, S. / Docquier, J.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.2 KB | Display | ![]() |
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PDB format | ![]() | 177.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 65.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eoeSC ![]() 5eooC ![]() 5euaC C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28921.693 Da / Num. of mol.: 4 / Fragment: UNP residues 19-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-ID1 / #4: Chemical | ChemComp-MRD / ( | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.46 % / Description: plate-shaped crystals |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG4600, 20% MPD, 0.1M sodium citrate, pH 5.6 / PH range: 5.6 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2013 |
Radiation | Monochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→51.68 Å / Num. obs: 91836 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 16.443 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.7 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EOE Resolution: 1.79→51.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.481 / SU ML: 0.078 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.119 / SU Rfree Cruickshank DPI: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.741 Å2
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Refine analyze | Luzzati coordinate error obs: 0.178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→51.68 Å
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Refine LS restraints |
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