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Yorodumi- PDB-6b22: Crystal structure OXA-24 beta-lactamase complexed with WCK 4234 b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b22 | ||||||
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Title | Crystal structure OXA-24 beta-lactamase complexed with WCK 4234 by co-crystallization | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / Inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | van den Akker, F. / Nguyen, N.Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2018 Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, ...Title: Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234. Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / ...Authors: Papp-Wallace, K.M. / Nguyen, N.Q. / Jacobs, M.R. / Bethel, C.R. / Barnes, M.D. / Kumar, V. / Bajaksouzian, S. / Rudin, S.D. / Rather, P.N. / Bhavsar, S. / Ravikumar, T. / Deshpande, P.K. / Patil, V. / Yeole, R. / Bhagwat, S.S. / Patel, M.V. / van den Akker, F. / Bonomo, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b22.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b22.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 6b22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/6b22 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/6b22 | HTTPS FTP |
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-Related structure data
Related structure data | 6b1fC 6b1hC 6b1jC 6b1wC 6b1xC 6b1yC C: citing same article (ref.) |
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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
#1: Protein | Mass: 27543.658 Da / Num. of mol.: 1 / Fragment: UNP residues 32-275 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 Production host: Escherichia coli (E. coli) / References: UniProt: Q8RLA6 | ||
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#2: Chemical | ChemComp-C8Y / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Calcium acetate, 0.2M Sodium cacodylate pH 6.5, and 18% PEG 8000. Inhibitor:protein molar ratio 1:50. Temp details: RT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→38.99 Å / Num. obs: 34171 / % possible obs: 99.3 % / Redundancy: 5.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.055 / Rrim(I) all: 0.138 / Net I/σ(I): 11.9 / Num. measured all: 198969 / Scaling rejects: 1348 |
Reflection shell | Resolution: 1.93→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.151 / Num. unique obs: 2247 / CC1/2: 0.656 / Rpim(I) all: 0.508 / Rrim(I) all: 1.261 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.973 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.101 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 87.64 Å2 / Biso mean: 24.027 Å2 / Biso min: 7.08 Å2
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Refinement step | Cycle: final / Resolution: 1.93→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.928→1.978 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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