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- PDB-6tzi: ADC-7 in complex with boronic acid transition state inhibitor PFC_001 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tzi | ||||||
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Title | ADC-7 in complex with boronic acid transition state inhibitor PFC_001 | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / inhibitor / Beta-lactamase / BATSI / ADC-7 | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fish, E.R. / Powers, R.A. / Wallar, B.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 306.6 KB | Display | ![]() |
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PDB format | ![]() | 246.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tzfC ![]() 6tzgC ![]() 6tzhC ![]() 6tzjC ![]() 4u0xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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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Components
#1: Protein | Mass: 40808.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-P1K / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.88 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 12, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07809 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.744→81.95 Å / Num. obs: 116473 / % possible obs: 96 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Net I/σ(I): 9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4U0X Resolution: 1.744→81.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.223 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.17 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.8 Å2 / Biso mean: 40.112 Å2 / Biso min: 18.45 Å2
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Refinement step | Cycle: final / Resolution: 1.744→81.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.744→1.789 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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