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Yorodumi- PDB-5vfd: Diazabicyclooctenone ETX2514 bound to Class D beta lactamase OXA-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vfd | ||||||
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Title | Diazabicyclooctenone ETX2514 bound to Class D beta lactamase OXA-24 from A. baumannii | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ETX2514 / beta-lactamase / PBP Gram negative / Astrazeneca / Entasis / A. baumannii / covalent inhibitor / 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 / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Olivier, N.B. / Lahiri, S. | ||||||
Citation | Journal: Nat Microbiol / Year: 2017 Title: ETX2514 is a broad-spectrum beta-lactamase inhibitor for the treatment of drug-resistant Gram-negative bacteria including Acinetobacter baumannii. Authors: Durand-Reville, T.F. / Guler, S. / Comita-Prevoir, J. / Chen, B. / Bifulco, N. / Huynh, H. / Lahiri, S. / Shapiro, A.B. / McLeod, S.M. / Carter, N.M. / Moussa, S.H. / Velez-Vega, C. / ...Authors: Durand-Reville, T.F. / Guler, S. / Comita-Prevoir, J. / Chen, B. / Bifulco, N. / Huynh, H. / Lahiri, S. / Shapiro, A.B. / McLeod, S.M. / Carter, N.M. / Moussa, S.H. / Velez-Vega, C. / Olivier, N.B. / McLaughlin, R. / Gao, N. / Thresher, J. / Palmer, T. / Andrews, B. / Giacobbe, R.A. / Newman, J.V. / Ehmann, D.E. / de Jonge, B. / O'Donnell, J. / Mueller, J.P. / Tommasi, R.A. / Miller, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vfd.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vfd.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vfd_validation.pdf.gz | 796 KB | Display | wwPDB validaton report |
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Full document | 5vfd_full_validation.pdf.gz | 796.8 KB | Display | |
Data in XML | 5vfd_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 5vfd_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/5vfd ftp://data.pdbj.org/pub/pdb/validation_reports/vf/5vfd | HTTPS FTP |
-Related structure data
Related structure data | 2jc7S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27586.660 Da / Num. of mol.: 1 / Mutation: K84KCX 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, A8G88_08245 Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8RLA6 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-9CP / ( | #4: Chemical | ChemComp-9CM / ( | #5: 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: 4.05 Å3/Da / Density % sol: 69.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Crystallization was achieved using 6 mg/mL of enzyme in 3 mg/mL of compound in 01. MES buffer (pH 6.0) containing 2.4 M (NH4)2SO4 as the precipitant solution |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→102.68 Å / Num. obs: 33764 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 24.758 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rsym value: 0.081 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 4 / Num. unique obs: 3993 / Rpim(I) all: 0.189 / Rsym value: 0.488 / % possible all: 80.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JC7 Resolution: 1.93→51.34 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.104
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Displacement parameters | Biso mean: 29.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.93→51.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Origin x: -24.8502 Å / Origin y: -7.0862 Å / Origin z: 10.9211 Å
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Refinement TLS group | Selection details: { A|* } |