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Yorodumi- PDB-6q35: Crystal structure of GES-5 beta-lactamase in complex with boronic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q35 | ||||||
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Title | Crystal structure of GES-5 beta-lactamase in complex with boronic inhibitor cpd 3 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / bacterial resistance / acyclic boronic inhibitors | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Maso, L. / Quotadamo, A. / Bellio, P. / Montanari, M. / Venturelli, A. / Celenza, G. / Costi, M.P. / Tondi, D. / Cendron, L. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2019 Title: X-ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid beta-Lactamase Inhibitors. Authors: Cendron, L. / Quotadamo, A. / Maso, L. / Bellio, P. / Montanari, M. / Celenza, G. / Venturelli, A. / Costi, M.P. / Tondi, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q35.cif.gz | 237.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q35.ent.gz | 189.6 KB | Display | PDB format |
PDBx/mmJSON format | 6q35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/6q35 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q35 | HTTPS FTP |
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-Related structure data
Related structure data | 6ibsC 6ibvC 6q2yC 6q30C 4gnuS 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: 29353.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Unobserved residues / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaGES-5, pGES-GZ_027 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09HD0, beta-lactamase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-DMS / #5: 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: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M NaBr; 0.1 M Bis Tris propane pH 8.5; 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→58.82 Å / Num. obs: 104301 / % possible obs: 99.98 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Net I/σ(I): 11.42 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 10332 / CC1/2: 0.812 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GNU Resolution: 1.4→58.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.635 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 20.522 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→58.82 Å
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Refine LS restraints |
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