+Open data
-Basic information
Entry | Database: PDB / ID: 6d19 | ||||||
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Title | Crystal structure of KPC-2 complexed with compound 9 | ||||||
Components | Carbapenem-hydrolyzing beta-lactamase KPC | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / beta-lactamase / carbapenemase / phosphonate / inhibitor / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex | ||||||
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 / molecular replacement / Resolution: 1.45 Å | ||||||
Authors | Pemberton, O.A. / Chen, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. Authors: Pemberton, O.A. / Jaishankar, P. / Akhtar, A. / Adams, J.L. / Shaw, L.N. / Renslo, A.R. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d19.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d19.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 6d19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/6d19 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/6d19 | HTTPS FTP |
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-Related structure data
Related structure data | 6d15C 6d16C 6d17C 6d18C 6d1aC 6d1bC 6d1cC 6d1dC 6d1eC 6d1fC 6d1gC 6d1hC 6d1iC 6d1jC 6d1kC 6dd0C 6dd1C 6ny7C 6o3rC 6o5tC 5ul8S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30806.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F663, beta-lactamase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 2.13 Å3/Da / Density % sol: 42.15 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium sulfate, 5% (v/v) Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.45→47.34 Å / Num. obs: 47304 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Rsym value: 0.086 / Net I/σ(I): 10.6 | ||||||||||||||||||||||||
Reflection shell | Rsym value: 0.058 / Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UL8 Resolution: 1.45→41.049 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.95 / Phase error: 21.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.35 Å2 / Biso mean: 30.7713 Å2 / Biso min: 14.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→41.049 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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