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- PDB-7me9: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 7me9 | ||||||
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Title | CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / Gram-positive / beta-lactamase / antibiotic resistance / inhibitor / avibactam | ||||||
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 | ![]() | 71.4 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.7 KB | Display | ![]() |
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Full document | ![]() | 448.5 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lnoSC ![]() 7lnqC ![]() 7lnrC ![]() 7meaC ![]() 7mebC ![]() 7mecC ![]() 7medC ![]() 7meeC ![]() 7mefC ![]() 7megC ![]() 7mehC S: Starting model for refinement 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
#1: Protein | Mass: 28617.234 Da / Num. of mol.: 1 / Mutation: K238A, K244A Source method: isolated from a genetically manipulated source Details: double lysine to alanine mutant Lys238Ala and Lys244Ala Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MPD / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % |
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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: Jun 28, 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: 1.7→39.1 Å / Num. obs: 36007 / % possible obs: 100 % / Redundancy: 23.6 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Rrim(I) all: 0.11 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1853 / CC1/2: 0.776 / Rpim(I) all: 0.35 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7LNO Resolution: 1.7→37.23 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.69 / 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: 94.6 Å2 / Biso mean: 27.8896 Å2 / Biso min: 14.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→37.23 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: 12 / % reflection obs: 100 %
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