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Yorodumi- PDB-6tzf: ADC-7 in complex with boronic acid transition state inhibitor S17079 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tzf | ||||||
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Title | ADC-7 in complex with boronic acid transition state inhibitor S17079 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / inhibitor / Beta-lactamase / BATSI / 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: 1.96 Å | ||||||
Authors | Fish, E.R. / Powers, R.A. / Wallar, B.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2020 Title: 1,2,3-Triazolylmethaneboronate: A Structure Activity Relationship Study of a Class of beta-Lactamase Inhibitors againstAcinetobacter baumanniiCephalosporinase. Authors: Caselli, E. / Fini, F. / Introvigne, M.L. / Stucchi, M. / Taracila, M.A. / Fish, E.R. / Smolen, K.A. / Rather, P.N. / Powers, R.A. / Wallar, B.J. / Bonomo, R.A. / Prati, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tzf.cif.gz | 291.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tzf.ent.gz | 232.9 KB | Display | PDB format |
PDBx/mmJSON format | 6tzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tzf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6tzf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6tzf_validation.xml.gz | 52 KB | Display | |
Data in CIF | 6tzf_validation.cif.gz | 72.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/6tzf ftp://data.pdbj.org/pub/pdb/validation_reports/tz/6tzf | HTTPS FTP |
-Related structure data
Related structure data | 6tzgC 6tzhC 6tziC 6tzjC 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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2 |
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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-KAS / #3: 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: 2.19 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ADC-7 (3mg/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-D / Wavelength: 1.07818 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 12, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07818 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.957→98.88 Å / Num. obs: 96293 / % possible obs: 94.6 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.029 / Rrim(I) all: 0.058 / Net I/σ(I): 13.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U0T Resolution: 1.96→98.88 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.421 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.18 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.9 Å2 / Biso mean: 40.318 Å2 / Biso min: 12.36 Å2
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Refinement step | Cycle: final / Resolution: 1.96→98.88 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: 1.96→2.008 Å / Rfactor Rfree error: 0
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