+Open data
-Basic information
Entry | Database: PDB / ID: 8sdn | ||||||
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Title | Crystal structure of PDC-3 Y221H beta-lactamase | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Pseudomonas-derived Cephalosporinase / antibiotic resistance | ||||||
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: 2.1 Å | ||||||
Authors | Kumar, V. / van den Akker, F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sdn.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sdn.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 8sdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sdn_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 8sdn_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 8sdn_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 8sdn_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/8sdn ftp://data.pdbj.org/pub/pdb/validation_reports/sd/8sdn | HTTPS FTP |
-Related structure data
Related structure data | 8sdlC 8sdrC 8sdsC 8sdtC 8sdvC 3s22S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Pseudomonas aeruginosa (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: Q4H482, beta-lactamase |
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#2: Chemical | ChemComp-IPA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.45 % |
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Crystal grow | Temperature: 293 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. Protein contained 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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 20364 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.923 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.42 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 1977 / CC1/2: 0.972 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S22 Resolution: 2.1→35.61 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.88 / SU B: 5.072 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.204 / 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: 61.61 Å2 / Biso mean: 15.98 Å2 / Biso min: 4.82 Å2
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Refinement step | Cycle: final / Resolution: 2.1→35.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0
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