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Open data
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Basic information
Entry | Database: PDB / ID: 3if6 | ||||||
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Title | Crystal structure of OXA-46 beta-lactamase from P. aeruginosa | ||||||
![]() | (OXA-46 oxacillinase) x 3 | ||||||
![]() | HYDROLASE / serine beta-lactamase | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Docquier, J.D. / Benvenuti, M. / Calderone, V. / Giuliani, F. / Kapetis, D. / De Luca, F. / Rossolini, G.M. / Mangani, S. | ||||||
![]() | ![]() Title: Crystal structure of the narrow-spectrum OXA-46 class D beta-lactamase: relationship between active-site lysine carbamylation and inhibition by polycarboxylates Authors: Docquier, J.D. / Benvenuti, M. / Calderone, V. / Giuliani, F. / Kapetis, D. / De Luca, F. / Rossolini, G.M. / Mangani, S. #1: Journal: Antimicrob.Agents Chemother. / Year: 2005 Title: OXA-46, a new class D beta-lactamase of narrow substrate specificity encoded by a blaVIM-1-containing integron from a Pseudomonas aeruginosa clinical isolate Authors: Giuliani, F. / Docquier, J.D. / Riccio, M.L. / Pagani, L. / Rossolini, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.9 KB | Display | ![]() |
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PDB format | ![]() | 132 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hbrS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 31140.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 31097.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 31140.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 407 molecules ![](data/chem/img/TLA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-P6G / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1M Na,K L-tartrate tetrahydrate, 50mM Hepes, 2-4%(v/v) PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 28, 2005 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→56.5 Å / Num. all: 48568 / Num. obs: 48227 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.2 / Redundancy: 8.8 % / Biso Wilson estimate: 42.418 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.78 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.2 / Num. unique all: 756 / Rsym value: 0.61 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HBR Resolution: 2.4→31.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.322 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.438 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.818 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→31.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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