+Open data
-Basic information
Entry | Database: PDB / ID: 5tg5 | ||||||
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Title | OXA-24/40 in Complex with Boronic Acid BA8 | ||||||
Components | Beta-lactamase | ||||||
Keywords | hydrolase/hydrolase inhibitor / Inhibitor / Complex / Lactamase / OXA / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information penicillin binding / cell wall organization / beta-lactamase activity / beta-lactamase Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Powers, R.A. / Werner, J.P. / Mitchell, J.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2017 Title: Exploring the potential of boronic acids as inhibitors of OXA-24/40 beta-lactamase. Authors: Werner, J.P. / Mitchell, J.M. / Taracila, M.A. / Bonomo, R.A. / Powers, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tg5.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tg5.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 5tg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tg5_validation.pdf.gz | 468 KB | Display | wwPDB validaton report |
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Full document | 5tg5_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 5tg5_validation.xml.gz | 14 KB | Display | |
Data in CIF | 5tg5_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/5tg5 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/5tg5 | HTTPS FTP |
-Related structure data
Related structure data | 5tg4C 5tg6C 5tg7C 3paeS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27671.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40 Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RLA6, beta-lactamase |
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-Non-polymers , 5 types, 179 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Chemical | ChemComp-MEE / | #6: 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: 4.15 Å3/Da / Density % sol: 70.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM TRIS-HCl, pH 8.5, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→102.97 Å / Num. obs: 45159 / % possible obs: 95 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PAE Resolution: 1.75→72.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.922 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.97 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→72.81 Å
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Refine LS restraints |
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