+Open data
-Basic information
Entry | Database: PDB / ID: 4s2k | ||||||
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Title | OXA-48 in complex with Avibactam at pH 7.5 | ||||||
Components | Beta-lactamase | ||||||
Keywords | hydrolase/antibiotic / inhibitor / beta-lactamase / hydrolase-antibiotic complex | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | King, D.T. / Strynadka, N.C.J. | ||||||
Citation | Journal: ACS Infect Dis / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s2k.cif.gz | 408.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s2k.ent.gz | 337.4 KB | Display | PDB format |
PDBx/mmJSON format | 4s2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/4s2k ftp://data.pdbj.org/pub/pdb/validation_reports/s2/4s2k | HTTPS FTP |
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-Related structure data
Related structure data | 4s2iC 4s2jC 4s2nC 4s2oC 4s2pC 3hbrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 |
-Components
#1: Protein | Mass: 30396.721 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, FP68_27275, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase #2: Chemical | ChemComp-NXL / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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