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- PDB-8sds: Crystal structure of PDC-3 Y221H beta-lactamase in complex with t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sds | ||||||
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Title | Crystal structure of PDC-3 Y221H beta-lactamase in complex with the boronic acid inhibitor LP-06 | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / Pseudomonas-derived Cephalosporinase / antibiotic resistance | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, V. / van den Akker, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Natural protein engineering in the Omega-loop: the role of Y221 in ceftazidime and ceftolozane resistance in Pseudomonas -derived cephalosporinase. Authors: Mack, A.R. / Kumar, V. / Taracila, M.A. / Mojica, M.F. / O'Shea, M. / Schinabeck, W. / Silver, G. / Hujer, A.M. / Papp-Wallace, K.M. / Chen, S. / Haider, S. / Caselli, E. / Prati, F. / van ...Authors: Mack, A.R. / Kumar, V. / Taracila, M.A. / Mojica, M.F. / O'Shea, M. / Schinabeck, W. / Silver, G. / Hujer, A.M. / Papp-Wallace, K.M. / Chen, S. / Haider, S. / Caselli, E. / Prati, F. / van den Akker, F. / Bonomo, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.7 KB | Display | ![]() |
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PDB format | ![]() | 72.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 794.3 KB | Display | ![]() |
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Full document | ![]() | 795.5 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sdlC ![]() 8sdnC ![]() 8sdrC ![]() 8sdtC ![]() 8sdvC ![]() 3s22S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 43394.168 Da / Num. of mol.: 1 / Mutation: Y221H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CB4 / |
#3: Chemical | ChemComp-IMD / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.54 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM Imidazole pH 7.0, 2-8% isopropyl alcohol (IPA), and 16-34% PEG 3350. The protein was in 10 mM HEPES pH 7.5, 150 mM NaCl and 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→28.04 Å / Num. obs: 43613 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.63→1.67 Å / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3117 / CC1/2: 0.897 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3S22 Resolution: 1.63→28.04 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.697 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.46 Å2 / Biso mean: 17.479 Å2 / Biso min: 9.28 Å2
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Refinement step | Cycle: final / Resolution: 1.63→28.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.672 Å / Rfactor Rfree error: 0
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