+Open data
-Basic information
Entry | Database: PDB / ID: 4wm9 | ||||||
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Title | Acinetobacter baumanii OXA-24 complex with Avibactam | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / class D carbapenemase / inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Mangani, S. / Benvenuti, M. / Docquier, J.-D. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Molecular Basis of Selective Inhibition and Slow Reversibility of Avibactam against Class D Carbapenemases: A Structure-Guided Study of OXA-24 and OXA-48. Authors: Lahiri, S.D. / Mangani, S. / Jahic, H. / Benvenuti, M. / Durand-Reville, T.F. / De Luca, F. / Ehmann, D.E. / Rossolini, G.M. / Alm, R.A. / Docquier, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wm9.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wm9.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/4wm9 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/4wm9 | HTTPS FTP |
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-Related structure data
Related structure data | 4wmcC 2jc7S 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27690.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40 Production host: Escherichia coli (E. coli) / References: UniProt: Q8RLA6 |
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-Non-polymers , 5 types, 89 molecules
#2: Chemical | ChemComp-NXL / ( | ||||
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#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CO2 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Enzyme (6 mg/mL) co-crystallized with avibactam (3 mg/mL) in 0.1 M MES buffer (pH 6.0) containing 2.4 M (NH4)2SO4 as precipitant. PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→55.82 Å / Num. obs: 17188 / % possible obs: 92.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 4 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JC7 Resolution: 2.4→31.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.967 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 90 Å2 / Biso mean: 28.732 Å2 / Biso min: 12.4 Å2
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Refinement step | Cycle: final / Resolution: 2.4→31.76 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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