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Yorodumi- PDB-5eph: Crystal structure of extended-spectrum beta-lactamase BEL-1 in co... -
+Open data
-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 | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE/ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex / extended-spectrum beta-lactamase / Pseudomonas aeruginosa | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | |||||||||
Authors | Pozzi, C. / Benvenuti, M. / De Luca, F. / Docquier, J.D. / Mangani, S. | |||||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eph.cif.gz | 223.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eph.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 5eph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eph_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5eph_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5eph_validation.xml.gz | 45 KB | Display | |
Data in CIF | 5eph_validation.cif.gz | 65.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/5eph ftp://data.pdbj.org/pub/pdb/validation_reports/ep/5eph | HTTPS FTP |
-Related structure data
Related structure data | 5eoeSC 5eooC 5euaC C: citing same article (ref.) S: Starting model for refinement |
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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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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.) Pseudomonas aeruginosa (bacteria) / Gene: bla(BEL1), blaBEL-1 / Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3SAW3, beta-lactamase #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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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