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- PDB-6d3g: PER-2 class A extended-spectrum beta-lactamase crystal structure ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d3g | |||||||||
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Title | PER-2 class A extended-spectrum beta-lactamase crystal structure in complex with avibactam at 2.4 Angstrom resolution | |||||||||
![]() | Beta-lactamase![]() | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / DBO / penicilloil-serine-transferase / ![]() ![]() | |||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Power, P. / Ruggiero, M. / Gutkind, G. / Bonomo, R. / Klinke, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights into the Inhibition of the Extended-Spectrum beta-Lactamase PER-2 by Avibactam. Authors: Ruggiero, M. / Papp-Wallace, K.M. / Brunetti, F. / Barnes, M.D. / Bonomo, R.A. / Gutkind, G. / Klinke, S. / Power, 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 | ![]() | 223.7 KB | Display | ![]() |
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PDB format | ![]() | 180.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6dguC ![]() 4d2oS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 30956.328 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NXL / ( ![]() #3: Chemical | ChemComp-PG4 / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 6000, 0.05 M imidazole pH=8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016 Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS |
Radiation | Monochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.398→48.17 Å / Num. obs: 46410 / % possible obs: 99.76 % / Redundancy: 6.65 % / Biso Wilson estimate: 55.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.092 / Net I/σ(I): 13.73 |
Reflection shell | Resolution: 2.4→2.54 Å / Redundancy: 6.65 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 7289 / CC1/2: 0.746 / Rrim(I) all: 1 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4D2O Resolution: 2.398→48.17 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.398→48.17 Å
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Refine LS restraints |
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LS refinement shell |
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