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- PDB-7a61: Crystal structure of KPC-2 with hydrolyzed faropenem (ring-open form) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a61 | ||||||
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Title | Crystal structure of KPC-2 with hydrolyzed faropenem (ring-open form) | ||||||
![]() | Carbapenem-hydrolyzing beta-lactamase KPC | ||||||
![]() | ANTIMICROBIAL PROTEIN / metallo-beta-lactamase / antibiotic / faropenem / catalysis | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tooke, C.L. / Hinchliffe, P. / Spencer, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Faropenem reacts with serine and metallo-beta-lactamases to give multiple products. Authors: Lucic, A. / Hinchliffe, P. / Malla, T.R. / Tooke, C.L. / Brem, J. / Calvopina, K. / Lohans, C.T. / Rabe, P. / McDonough, M.A. / Armistead, T. / Orville, A.M. / Spencer, J. / Schofield, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.9 KB | Display | ![]() |
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PDB format | ![]() | 147.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 762.4 KB | Display | ![]() |
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Full document | ![]() | 763.1 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a5zC ![]() 7a60C ![]() 7a63C ![]() 6qw9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30805.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-R0B / ( | ||||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 5% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89996 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→48.28 Å / Num. obs: 75948 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 11.81 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.046 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.25→1.27 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3711 / CC1/2: 0.703 / Rpim(I) all: 0.823 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QW9 Resolution: 1.25→48.28 Å / SU ML: 0.1387 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7566 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→48.28 Å
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Refine LS restraints |
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LS refinement shell |
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