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Open data
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Basic information
Entry | Database: PDB / ID: 7med | ||||||
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Title | CDD-1 beta-lactamase in imidazole/MPD 5 minute avibactam complex | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE/INHIBITOR / Gram-positive / beta-lactamase / antibiotic resistance / inhibitor / avibactam / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smith, C.A. / Vakulenko, S.B. | ||||||
![]() | ![]() Title: In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D beta-lactamases. Authors: Stewart, N.K. / Toth, M. / Stasyuk, A. / Vakulenko, S.B. / Smith, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.7 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808 KB | Display | ![]() |
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Full document | ![]() | 810 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lnoC ![]() 7lnqC ![]() 7lnrC ![]() 7me9C ![]() 7meaC ![]() 7mebC ![]() 7mecC ![]() 7meeC ![]() 7mefC ![]() 7megC ![]() 7mehC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 28617.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: double lysine to alanine mutant Lys238Ala and Lys244Ala Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 156 molecules ![](data/chem/img/NXL.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NXL / ( | ||||
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#3: Chemical | ChemComp-CO2 / | ||||
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.08 % |
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Crystal grow | Temperature: 277 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→39.03 Å / Num. obs: 31415 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 1 / Rpim(I) all: 0.018 / Rrim(I) all: 0.092 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.78→1.82 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1757 / CC1/2: 0.733 / Rpim(I) all: 0.435 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 99.27 Å2 / Biso mean: 30.2631 Å2 / Biso min: 14.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.78→39.03 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: 11
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