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Yorodumi- PDB-5eua: Crystal structure of extended-spectrum beta-lactamase BEL-1 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eua | |||||||||
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Title | Crystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Moxalactam | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE/ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex / extended-spectrum beta-lactamase / Pseudomonas aeruginosa / oxacephem antibiotic | |||||||||
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: 1.85 Å | |||||||||
Authors | Pozzi, C. / De Luca, F. / Benvenuti, M. / 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 | 5eua.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eua.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 5eua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eua_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5eua_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5eua_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5eua_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5eua ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5eua | HTTPS FTP |
-Related structure data
Related structure data | 5eoeSC 5eooC 5ephC 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
#1: Protein | Mass: 28921.693 Da / Num. of mol.: 2 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 | #3: Chemical | #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: 2.2 Å3/Da / Density % sol: 44.21 % |
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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: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2013 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→33.58 Å / Num. obs: 42901 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 19.68 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EOE Resolution: 1.85→33.58 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.153 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Moxalactam in B subunit was only partially modeled due to positional disorder
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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: 27.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→33.58 Å
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Refine LS restraints |
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