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- PDB-6g0k: Crystal structure of Enterococcus faecium D63r Penicillin-Binding... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6g0k | ||||||
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Title | Crystal structure of Enterococcus faecium D63r Penicillin-Binding protein 5 (PBP5fm) | ||||||
![]() | Low affinity penicillin-binding protein 5 (PBP5) | ||||||
![]() | ANTIBIOTIC / penicillin-binding / ceftobiprole / Enterococcus faecium / Antibiotic resistance | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sauvage, E. / El Gachi, M. / Herman, R. / Kerff, F. / Charlier, P. | ||||||
![]() | ![]() Title: Structural basis of inactivation of Enterococcus faecium penicillin binding protein 5 by ceftobiprole. Authors: Sauvage, E. / El Gachi, M. / Kerff, F. / Herman, R. / Verlaine, O. / Amoroso, A. / Page, M.G.P. / Joris, B. / Charlier, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 630.7 KB | Display | ![]() |
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PDB format | ![]() | 528.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.2 KB | Display | ![]() |
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Full document | ![]() | 495.6 KB | Display | |
Data in XML | ![]() | 61.3 KB | Display | |
Data in CIF | ![]() | 83.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 70743.773 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-SO4 / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.97 % |
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Crystal grow | Temperature: 292 K / Method: evaporation Details: Crystals were grown by the sitting-drop vapor diffusion method. Crystals were grown at 20C by mixing 1microL of PBP5fm (48 mg/ml), 2microL of reservoir (20% PEG8000 (w/v), 0.4 M Li2SO4 and ...Details: Crystals were grown by the sitting-drop vapor diffusion method. Crystals were grown at 20C by mixing 1microL of PBP5fm (48 mg/ml), 2microL of reservoir (20% PEG8000 (w/v), 0.4 M Li2SO4 and 100 mM Na acetate at pH 4.5) and 0.5 microL of 0.1M ceftobiprole (kind gift of Basilea Pharmaceutica. The crystal was cryoprotected in the same buffer containing 20 % (v/v) glycerol. Crystals were soaked for 5 min in 1 microl of 0.1 M ceftobiprole before cryoprotection. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.142 Å / Num. obs: 52908 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.095 / Rrim(I) all: 0.186 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7679 / Rpim(I) all: 0.481 / Rrim(I) all: 0.93 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→47.142 Å
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Refine LS restraints |
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LS refinement shell |
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