+Open data
-Basic information
Entry | Database: PDB / ID: 7qqc | ||||||
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Title | Structure of CTX-M-15 K73A mutant | ||||||
Components | Beta-lactamase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / beta-lactamase / mutant / antibiotic resistance | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae IS53 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.95 Å | ||||||
Authors | Tooke, C.L. / Hinchliffe, P. / Spencer, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mbio / Year: 2022 Title: Penicillanic Acid Sulfones Inactivate the Extended-Spectrum beta-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: an Alternative Mechanism of beta-Lactamase Inhibition. Authors: Hinchliffe, P. / Tooke, C.L. / Bethel, C.R. / Wang, B. / Arthur, C. / Heesom, K.J. / Shapiro, S. / Schlatzer, D.M. / Papp-Wallace, K.M. / Bonomo, R.A. / Spencer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qqc.cif.gz | 208 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qqc.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qqc_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 7qqc_full_validation.pdf.gz | 437 KB | Display | |
Data in XML | 7qqc_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 7qqc_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqc ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqc | HTTPS FTP |
-Related structure data
Related structure data | 6z7hC 6z7iC 6z7jC 6z7kC 7bdrC 7bdsC 7qq5C 7r3qC 7r3rC 6qw8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28234.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae IS53 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: W1EPV7, beta-lactamase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.68 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.72 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→42.43 Å / Num. obs: 151252 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 8.53 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 0.95→0.97 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7462 / CC1/2: 0.368 / Rpim(I) all: 0.794 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6QW8 Resolution: 0.95→35.91 Å / SU ML: 0.1232 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1594 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→35.91 Å
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Refine LS restraints |
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LS refinement shell |
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