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Yorodumi- PDB-5wi3: Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wi3 | |||||||||
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Title | Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to cefotaxime | |||||||||
Components | OXA-239 | |||||||||
Keywords | HYDROLASE / beta-lactamase / antibiotic resistance | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Acinetobacter sp. enrichment culture clone 8407 (environmental samples) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | |||||||||
Authors | Harper, T.M. / June, C.M. / Powers, R.A. / Leonard, D.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochem. J. / Year: 2018 Title: Multiple substitutions lead to increased loop flexibility and expanded specificity in Acinetobacter baumannii carbapenemase OXA-239. Authors: Harper, T.M. / June, C.M. / Taracila, M.A. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wi3.cif.gz | 211.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wi3.ent.gz | 166.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wi3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5wi3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5wi3_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5wi3_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/5wi3 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/5wi3 | HTTPS FTP |
-Related structure data
Related structure data | 5wi7C 5wibC 4k0xS S: Starting model for refinement 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 31 - 273 / Label seq-ID: 11 - 253
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-Components
#1: Protein | Mass: 28786.166 Da / Num. of mol.: 2 / Mutation: K82D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. enrichment culture clone 8407 (environmental samples) Gene: OXA-239 / Variant: K82D / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6YCI1, beta-lactamase #2: Chemical | #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: 2.7 Å3/Da / Density % sol: 54.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 100 mM NaH2PO4, 100 mM citric acid, 200 mM NaCl, 20% PEG 8000, pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07814 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07814 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→98.1 Å / Num. obs: 57689 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.046 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.811→1.817 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 542 / CC1/2: 0.873 / Rpim(I) all: 0.505 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K0X Resolution: 1.81→80.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.389 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.969 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→80.9 Å
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Refine LS restraints |
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