+Open data
-Basic information
Entry | Database: PDB / ID: 4wmc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | OXA-48 covalent complex with Avibactam inhibitor | |||||||||
Components | (Beta-lactamase) x 2 | |||||||||
Keywords | HYDROLASE / OXA-48 / Class D carbapenemase / Avibactam / inhibitor | |||||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wmc.cif.gz | 387.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wmc.ent.gz | 316.4 KB | Display | PDB format |
PDBx/mmJSON format | 4wmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wmc_validation.pdf.gz | 678.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4wmc_full_validation.pdf.gz | 727.6 KB | Display | |
Data in XML | 4wmc_validation.xml.gz | 72.1 KB | Display | |
Data in CIF | 4wmc_validation.cif.gz | 96.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/4wmc ftp://data.pdbj.org/pub/pdb/validation_reports/wm/4wmc | HTTPS FTP |
-Related structure data
Related structure data | 4wm9C 3hbrS 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: 28054.768 Da / Num. of mol.: 6 / Fragment: UNP residues 24-265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase #2: Protein | Mass: 28097.770 Da / Num. of mol.: 2 / Fragment: UNP residues 24-265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase #3: Chemical | ChemComp-NXL / ( #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 10% PEG8000, 5-8% 1-butanol, 10 mg/mL OXA-48, and 3 mg/mL avibactam |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9834 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9834 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→65.8 Å / Num. obs: 99733 / % possible obs: 93.4 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.9 / Num. unique all: 12691 / % possible all: 88 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HBR Resolution: 2.3→63.88 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.862 / SU B: 8.172 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.418 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.71 Å2 / Biso min: 2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→63.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
|