+Open data
-Basic information
Entry | Database: PDB / ID: 7keq | ||||||
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Title | avibactam-CDD-1 6 minute complex | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/INHIBITOR / antibiotic resistance / mutant / Gram-positive / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Smith, C.A. / Vakulenko, S.B. / Stewart, N.K. / Toth, M. | ||||||
Citation | Journal: Acs Infect Dis. / Year: 2021 Title: Inhibition of the Clostridioides difficile Class D beta-Lactamase CDD-1 by Avibactam. Authors: Stewart, N.K. / Toth, M. / Stasyuk, A. / Lee, M. / Smith, C.A. / Vakulenko, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7keq.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7keq.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 7keq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/7keq ftp://data.pdbj.org/pub/pdb/validation_reports/ke/7keq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36043.055 Da / Num. of mol.: 1 / Mutation: K238A, K244A Source method: isolated from a genetically manipulated source Details: Class D beta-lactamase / Source: (gene. exp.) Clostridioides difficile (bacteria) Gene: blaR1_4, blaR1_1, E5F39_11445, SAMEA2239407_03320, SAMEA3374989_01677 Production host: Escherichia coli (E. coli) / References: UniProt: A0A160YKM3, beta-lactamase |
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-Non-polymers , 5 types, 162 molecules
#2: Chemical | ChemComp-NXL / ( | ||||
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#3: Chemical | ChemComp-FYG / ( | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.0, 2.4 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.195 Å |
Detector | Type: RAYONIX MX-325 / Detector: CCD / Date: Jun 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.195 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.1 Å / Num. obs: 22396 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 32.1 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.044 / Rrim(I) all: 0.145 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 1615 / CC1/2: 0.718 / Rpim(I) all: 0.41 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→39.07 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.75 / Stereochemistry target values: ML
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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 max: 87.02 Å2 / Biso mean: 31.5829 Å2 / Biso min: 16.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→39.07 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
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