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Yorodumi- PDB-5w12: ADC-7 in complex with boronic acid transition state inhibitor EC04 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w12 | ||||||
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Title | ADC-7 in complex with boronic acid transition state inhibitor EC04 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / inhibitor / Beta-lactamase / BATSI / EC04 / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Smolen, K.A. / Powers, R.A. / Wallar, B.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Infect Dis / Year: 2018 Title: Inhibition of Acinetobacter-Derived Cephalosporinase: Exploring the Carboxylate Recognition Site Using Novel beta-Lactamase Inhibitors. Authors: Caselli, E. / Romagnoli, C. / Powers, R.A. / Taracila, M.A. / Bouza, A.A. / Swanson, H.C. / Smolen, K.A. / Fini, F. / Wallar, B.J. / Bonomo, R.A. / Prati, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w12.cif.gz | 298.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w12.ent.gz | 239.6 KB | Display | PDB format |
PDBx/mmJSON format | 5w12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/5w12 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w12 | HTTPS FTP |
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-Related structure data
Related structure data | 5w13C 5w14C 4u0tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DRA1, beta-lactamase #2: Chemical | ChemComp-9TG / #3: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.87 % |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→98.285 Å / Num. obs: 113662 / % possible obs: 99 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.88→1.886 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1169 / CC1/2: 0.734 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U0T Resolution: 1.88→98.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.708 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.22 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→98.28 Å
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Refine LS restraints |
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