[English] 日本語
Yorodumi- PDB-6d3g: PER-2 class A extended-spectrum beta-lactamase crystal structure ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d3g | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | PER-2 class A extended-spectrum beta-lactamase crystal structure in complex with avibactam at 2.4 Angstrom resolution | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / DBO / penicilloil-serine-transferase / antibiotic resistance / 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 | Citrobacter freundii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å | |||||||||
Authors | Power, P. / Ruggiero, M. / Gutkind, G. / Bonomo, R. / Klinke, S. | |||||||||
Funding support | Argentina, 2items
| |||||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2019 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6d3g.cif.gz | 223.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6d3g.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 6d3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/6d3g ftp://data.pdbj.org/pub/pdb/validation_reports/d3/6d3g | HTTPS FTP |
---|
-Related structure data
Related structure data | 6dguC 4d2oS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30956.328 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: blaPER-2 / Plasmid: pET28/PER-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2RP81, beta-lactamase #2: Chemical | ChemComp-NXL / ( #3: Chemical | ChemComp-PG4 / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
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: 0.9801 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|