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Yorodumi- PDB-6ibs: Crystal structure of NDM-1 beta-lactamase in complex with boronic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ibs | ||||||
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Title | Crystal structure of NDM-1 beta-lactamase in complex with boronic inhibitor cpd 6 | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE / beta-lactamase / bacterial resistance / acyclic boronic inhibitors | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 | 6ibs.cif.gz | 205 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ibs.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ibs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/6ibs ftp://data.pdbj.org/pub/pdb/validation_reports/ib/6ibs | HTTPS FTP |
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-Related structure data
Related structure data | 6ibvC 6q2yC 6q30C 6q35C 5zguS 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: 25860.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The electron density maps allow the reconstruction of these residues only. Those missing are unobserved regions Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-CA / #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: 1.94 Å3/Da / Density % sol: 36.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE |
-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 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→42.59 Å / Num. obs: 83133 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.026 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.37→1.419 Å / Rmerge(I) obs: 0.488 / Num. unique obs: 4061 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZGU Resolution: 1.37→42.59 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.825 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.051 / 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: 14.042 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→42.59 Å
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Refine LS restraints |
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