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Open data
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Basic information
Entry | Database: PDB / ID: 4s2k | ||||||
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Title | OXA-48 in complex with Avibactam at pH 7.5 | ||||||
![]() | Beta-lactamase | ||||||
![]() | hydrolase/antibiotic / inhibitor / beta-lactamase / hydrolase-antibiotic complex | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | King, D.T. / Strynadka, N.C.J. | ||||||
![]() | ![]() Title: Molecular Mechanism of Avibactam-Mediated beta-Lactamase Inhibition. Authors: King, D.T. / King, A.M. / Lal, S.M. / Wright, G.D. / Strynadka, N.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 408.9 KB | Display | ![]() |
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PDB format | ![]() | 337.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 57.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4s2iC ![]() 4s2jC ![]() 4s2nC ![]() 4s2oC ![]() 4s2pC ![]() 3hbrS 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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Unit cell |
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Details | Authors report that the protein behaves as a dimer in solution as determined by gel filtration |
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Components
#1: Protein | Mass: 30396.721 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NXL / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.52 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM tris pH 7.5, 0.1M ammonium chloride, 40% MPD, 5% PEG 8K, 100 mM NaCl, 2 mM avibactam, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013 |
Radiation | Monochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→52.42 Å / Num. all: 69789 / Num. obs: 69650 / % possible obs: 99.8 % / Biso Wilson estimate: 28.8 Å2 |
Reflection shell | Resolution: 2.1→2.21 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HBR Resolution: 2.1→42.25 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.9198 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 30.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.253 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→42.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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