+Open data
-Basic information
Entry | Database: PDB / ID: 4wyy | ||||||
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Title | Crystal Structure of P. aeruginosa AmpC | ||||||
Components | Beta-lactamase | ||||||
Keywords | hydrolase/hydrolase inhibitor / Beta lactamase / inhibitor / 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Ferguson, A.D. | ||||||
Citation | Journal: ACS Infect Dis / Year: 2015 Title: 4,5-Disubstituted 6-Aryloxy-1,3-dihydrobenzo[c][1,2]oxaboroles Are Broad-Spectrum Serine beta-Lactamase Inhibitors. Authors: McKinney, D.C. / Zhou, F. / Eyermann, C.J. / Ferguson, A.D. / Prince, D.B. / Breen, J. / Giacobbe, R.A. / Lahiri, S. / Verheijen, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wyy.cif.gz | 161.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wyy.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 4wyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/4wyy ftp://data.pdbj.org/pub/pdb/validation_reports/wy/4wyy | HTTPS FTP |
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-Related structure data
Related structure data | 4wz4C 4wz5C 4ooyS 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
#1: Protein | Mass: 39499.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: ampC, PA4110 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P24735, beta-lactamase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-3VT / [( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 10% isopropanol, 100 mM imidazole / PH range: 6.6 - 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→53.12 Å / Num. obs: 84509 / Biso Wilson estimate: 13.84 Å2 |
Reflection shell | Resolution: 1.28→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.4 / % possible all: 78.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OOY Resolution: 1.28→53.12 Å / Cor.coef. Fo:Fc: 0.9562 / Cor.coef. Fo:Fc free: 0.9433 / SU R Cruickshank DPI: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.048 / SU Rfree Blow DPI: 0.051 / SU Rfree Cruickshank DPI: 0.049
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Displacement parameters | Biso mean: 19.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.136 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→53.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.28→1.31 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -6.206 Å / Origin y: -2.987 Å / Origin z: 17.7378 Å
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Refinement TLS group | Selection details: { A|* } |