+Open data
-Basic information
Entry | Database: PDB / ID: 6pwm | ||||||
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Title | ADC-7 in complex with Beta-lactam antibiotic ceftazidime | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / substrate / Beta-lactamase / antibiotic / ADC-7. | ||||||
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 | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Curtis, B.C. / Powers, R.A. / Wallar, B.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2020 Title: Structural Insights into Inhibition of the Acinetobacter-Derived Cephalosporinase ADC-7 by Ceftazidime and Its Boronic Acid Transition State Analog. Authors: Curtis, B.N. / Smolen, K.A. / Barlow, S.J. / Caselli, E. / Prati, F. / Taracila, M.A. / Bonomo, R.A. / Wallar, B.J. / 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 | 6pwm.cif.gz | 292.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pwm.ent.gz | 234.9 KB | Display | PDB format |
PDBx/mmJSON format | 6pwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pwm_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6pwm_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6pwm_validation.xml.gz | 52 KB | Display | |
Data in CIF | 6pwm_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/6pwm ftp://data.pdbj.org/pub/pdb/validation_reports/pw/6pwm | HTTPS FTP |
-Related structure data
Related structure data | 6pwlC 4u0tS 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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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 40808.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DRA1, beta-lactamase #2: Chemical | ChemComp-CAZ / #3: Chemical | ChemComp-GLY / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ADC-7 (3.5mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→97.135 Å / Num. obs: 55876 / % possible obs: 98.7 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.4→2.408 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 545 / CC1/2: 0.782 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U0T Resolution: 2.4→85.32 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.967 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.667 / ESU R Free: 0.29 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 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.94 Å2 / Biso mean: 48.052 Å2 / Biso min: 7.44 Å2
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Refinement step | Cycle: final / Resolution: 2.4→85.32 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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