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Yorodumi- PDB-4gzb: Crystal structure of native AmpC beta-lactamase from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gzb | ||||||
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Title | Crystal structure of native AmpC beta-lactamase from Pseudomonas aeruginosa PAO1 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase fold / antibiotic resistance | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Benvenuti, M. / De Luca, F. / Docquier, J.D. / Mangani, S. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2013 Title: Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC beta-lactamases Authors: Lahiri, S.D. / Mangani, S. / Durand-Reville, T. / Benvenuti, M. / De Luca, F. / Sanyal, G. / 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 | 4gzb.cif.gz | 156.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gzb.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 4gzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gzb_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 4gzb_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 4gzb_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4gzb_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/4gzb ftp://data.pdbj.org/pub/pdb/validation_reports/gz/4gzb | HTTPS FTP |
-Related structure data
Related structure data | 4hbtC 4hbuC 4hefC 1ke4S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 40723.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: ampC, blaAmpC, PA4110 / Plasmid: pET-AmpC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24735, beta-lactamase |
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#2: Chemical | ChemComp-EDO / |
#3: 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: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 20% PEG 8000, O.1M K2HPO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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 315r / Detector: CCD / Date: Dec 5, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→46.617 Å / Num. all: 38317 / Num. obs: 38317 / % possible obs: 83.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 26.695 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.8 / Num. unique all: 9784 / % possible all: 82.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KE4 Resolution: 1.79→34.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.065 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.534 Å2
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Refine analyze | Luzzati coordinate error obs: 0.132 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→34.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.836 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -35.2493 Å / Origin y: 12.2298 Å / Origin z: -14.3113 Å
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