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Yorodumi- PDB-4hbu: Crystal structure of CTX-M-15 extended-spectrum beta-lactamase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hbu | ||||||
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Title | Crystal structure of CTX-M-15 extended-spectrum beta-lactamase in complex with avibactam (NXL104) | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Hydrolysis of beta-lactams / Antibiotic resistance / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Docquier, J.D. / Benvenuti, M. / Bruneau, J.M. / Rossolini, G.M. / Miossec, C. / Black, M.T. / 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 | 4hbu.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hbu.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 4hbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hbu_validation.pdf.gz | 788 KB | Display | wwPDB validaton report |
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Full document | 4hbu_full_validation.pdf.gz | 790.6 KB | Display | |
Data in XML | 4hbu_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 4hbu_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/4hbu ftp://data.pdbj.org/pub/pdb/validation_reports/hb/4hbu | HTTPS FTP |
-Related structure data
Related structure data | 4gzbC 4hbtSC 4hefC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28138.826 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: blaUOE-1, bla, bla CTX-M-15, blaCTX-M-15, blaCTX-M15, CTX-M-15 Production host: Escherichia coli (E. coli) / References: UniProt: Q9EXV5, beta-lactamase |
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-Non-polymers , 5 types, 328 molecules
#2: Chemical | ChemComp-NXL / ( | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / #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: 2.13 Å3/Da / Density % sol: 42.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris-HCl, 2.2-2.4M ammonium sulfate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.918 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2009 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→23.54 Å / Num. all: 98124 / Num. obs: 98124 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.1→1.16 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HBT Resolution: 1.1→22.84 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.424 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.278 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→22.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
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