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Yorodumi- PDB-5eoe: Crystal structure of extended-spectrum beta-lactamase BEL-1 (orth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eoe | |||||||||
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Title | Crystal structure of extended-spectrum beta-lactamase BEL-1 (orthorhombic form) | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / Extended-Spectrum Beta-Lactamase / citrate / native / 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: 1.6 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 | 5eoe.cif.gz | 140.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eoe.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 5eoe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eoe_validation.pdf.gz | 493 KB | Display | wwPDB validaton report |
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Full document | 5eoe_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 5eoe_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 5eoe_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/5eoe ftp://data.pdbj.org/pub/pdb/validation_reports/eo/5eoe | HTTPS FTP |
-Related structure data
Related structure data | 5eooC 5ephC 5euaC 1iysS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28722.486 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla(BEL1), blaBEL-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3SAW3, beta-lactamase |
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-Non-polymers , 8 types, 816 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-1PE / | #6: Chemical | #7: Chemical | ChemComp-MRD / ( | #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.87 % / Description: Plate-shaped crystals |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 15% PEG 4000, 15% 2-propanol, 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: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 20, 2007 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.25 Å / Num. obs: 86406 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Biso Wilson estimate: 14.112 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 6.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IYS Resolution: 1.6→29.25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.194 / SU ML: 0.042 / SU R Cruickshank DPI: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / SU Rfree Cruickshank DPI: 0.068 / 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: 14.585 Å2
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Refine analyze | Luzzati coordinate error obs: 0.145 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→29.25 Å
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Refine LS restraints |
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