+Open data
-Basic information
Entry | Database: PDB / ID: 7b3s | ||||||
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Title | OXA-10 beta-lactamase with S67Dha modification | ||||||
Components | Beta-lactamase OXA-10 | ||||||
Keywords | HYDROLASE / beta lactamase / antibiotic resistance / tazobactam / dehydroalanine / irreversible inhibition | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Lang, P.A. / Brem, J. / Schofield, C.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Studies on enmetazobactam clarify mechanisms of widely used beta-lactamase inhibitors. Authors: Lang, P.A. / Raj, R. / Tumber, A. / Lohans, C.T. / Rabe, P. / Robinson, C.V. / Brem, J. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b3s.cif.gz | 218.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b3s.ent.gz | 171.4 KB | Display | PDB format |
PDBx/mmJSON format | 7b3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b3s_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 7b3s_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 7b3s_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 7b3s_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/7b3s ftp://data.pdbj.org/pub/pdb/validation_reports/b3/7b3s | HTTPS FTP |
-Related structure data
Related structure data | 6t35C 7b3rC 7b3uC 1k55S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27680.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14489, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.7 Å3/Da / Density % sol: 54.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium sulfate, 0.1 M Bis-Tris propane pH 7.5, 20 % (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.849→48.87 Å / Num. obs: 52193 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.278 / Rpim(I) all: 0.08 / Rrim(I) all: 0.29 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K55 Resolution: 1.85→48.602 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.62 Å2 / Biso mean: 23.7046 Å2 / Biso min: 5.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→48.602 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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