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Yorodumi- PDB-6bn3: CTX-M-151 class A extended-spectrum beta-lactamase apo crystal st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bn3 | |||||||||
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Title | CTX-M-151 class A extended-spectrum beta-lactamase apo crystal structure at 1.3 Angstrom resolution | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / Beta-lactamase / penicilloil-serine-transferase / antibiotic resistance | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Salmonella enterica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.278 Å | |||||||||
Authors | Power, P. / Ghiglione, B. / Rodriguez, M.M. / Gutkind, G. / Ishii, Y. / Bonomo, R.A. / Klinke, S. | |||||||||
Funding support | Argentina, 2items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2021 Title: Structural and Biochemical Characterization of the Novel CTX-M-151 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam. Authors: Ghiglione, B. / Rodriguez, M.M. / Brunetti, F. / Papp-Wallace, K.M. / Yoshizumi, A. / Ishii, Y. / Bonomo, R.A. / Gutkind, G. / Klinke, S. / Power, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bn3.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bn3.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/6bn3 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/6bn3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28529.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: blaCTX-M151 / Plasmid: pET28/151 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A077KT80, beta-lactamase |
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#2: Chemical | ChemComp-EPE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.75 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 8000, 0.1 M Hepes, pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016 Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS |
Radiation | Monochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.278→47.77 Å / Num. obs: 56873 / % possible obs: 98.14 % / Redundancy: 6.5 % / Net I/σ(I): 12.5 |
-Processing
Software |
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Refinement | Resolution: 1.278→47.77 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.95 Å2 / Biso mean: 25.57 Å2 / Biso min: 13.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.278→47.77 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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