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Yorodumi- PDB-5ll7: Crystal structure of KPC-2 carbapenemase in complex with a phenyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ll7 | ||||||
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Title | Crystal structure of KPC-2 carbapenemase in complex with a phenyl boronic inhibitor. | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / carbapenemase / beta-lactamase / phenyl boronic inhibitor | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Vicario, M. / Celenza, G. / Bellio, P. / Perilli, M.G. / Tondi, D. / Cendron, L. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Chemmedchem / Year: 2018 Title: Phenylboronic Acid Derivatives as Validated Leads Active in Clinical Strains Overexpressing KPC-2: A Step against Bacterial Resistance. Authors: Celenza, G. / Vicario, M. / Bellio, P. / Linciano, P. / Perilli, M. / Oliver, A. / Blazquez, J. / Cendron, L. / Tondi, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ll7.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ll7.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ll7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ll7_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 5ll7_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 5ll7_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 5ll7_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/5ll7 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/5ll7 | HTTPS FTP |
-Related structure data
Related structure data | 5mgiC 3c5aS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28390.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaKPC-18 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H4IUK8, beta-lactamase | ||
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#2: Chemical | ChemComp-6YV / (~{ | ||
#3: Chemical | #4: 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: 2.05 Å3/Da / Density % sol: 40.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 15% polyethylene glycol 6000 (PEG 6000), 200mM potassium thiocyanate (KSCN), 100 mM sodium citrate (pH 4) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97778 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→40.565 Å / Num. obs: 46694 / % possible obs: 98.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C5A Resolution: 1.4→40.565 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 1.4→40.565 Å
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