|Entry||Database: PDB / ID: 6g0k|
|Title||Crystal structure of Enterococcus faecium D63r Penicillin-Binding protein 5 (PBP5fm)|
|Components||Low affinity penicillin-binding protein 5 (PBP5)|
|Keywords||ANTIBIOTIC / penicillin-binding / ceftobiprole / Enterococcus faecium / Antibiotic resistance|
|Function / homology|
Function and homology information
penicillin binding / response to antibiotic / membrane => GO:0016020 / plasma membrane
Similarity search - Function
NTF2-like N-terminal transpeptidase domain / NTF2-like N-terminal transpeptidase / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / NTF2-like domain superfamily / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Low affinity penicillin-binding protein 5 (PBP5)
Similarity search - Component
|Biological species||Enterococcus faecium (unknown)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å|
|Authors||Sauvage, E. / El Gachi, M. / Herman, R. / Kerff, F. / Charlier, P.|
|Citation||Journal: To Be Published|
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.
|Structure viewer||Molecule: |
Downloads & links
A: Low affinity penicillin-binding protein 5 (PBP5)
B: Low affinity penicillin-binding protein 5 (PBP5)
C: Low affinity penicillin-binding protein 5 (PBP5)
Mass: 70743.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (unknown) / Gene: pbp5 / Production host: Enterococcus faecium (unknown) / Strain (production host): D63r / References: UniProt: Q47759
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 3 Å3/Da / Density % sol: 58.97 %|
|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.
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å|
|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|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.142 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.92 |
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Refinement step||Cycle: LAST / Resolution: 2.9→47.142 Å|
|Refine LS restraints|
|LS refinement shell|
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