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- PDB-5wag: ADC-7 in complex with boronic acid transition state inhibitor S06017 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wag | ||||||
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Title | ADC-7 in complex with boronic acid transition state inhibitor S06017 | ||||||
![]() | Beta-lactamase![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() ![]() ![]() | ||||||
Function / homology | ![]() antibiotic catabolic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Powers, R.A. / Wallar, B.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter-Derived Cephalosporinase-7, a Unique Class C beta-Lactamase. Authors: Bouza, A.A. / Swanson, H.C. / Smolen, K.A. / VanDine, A.L. / Taracila, M.A. / Romagnoli, C. / Caselli, E. / Prati, F. / Bonomo, R.A. / Powers, R.A. / Wallar, B.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.1 KB | Display | ![]() |
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PDB format | ![]() | 234.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5wacC ![]() 5wadC ![]() 5waeC ![]() 5wafC ![]() 4u0tS 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 40808.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-A0V / #3: Chemical | ChemComp-SIN / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.11 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ADC-7 (3mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.931→81.397 Å / Num. obs: 99952 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.931→1.938 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 952 / CC1/2: 0.709 / % possible all: 95.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4U0T Resolution: 1.931→81.397 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.567 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.171 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.98 Å2
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Refinement step | Cycle: 1 / Resolution: 1.931→81.397 Å
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Refine LS restraints |
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