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- PDB-8peb: OXA-48_Q5. Epistasis Arises from Shifting the Rate-Limiting Step ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8peb | ||||||
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Title | OXA-48_Q5. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / Protein evolution. Antibiotic resistance. OXA-48. | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leiros, H.-K.S. / Frohlich, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: Epistasis arises from shifting the rate-limiting step during enzyme evolution of a beta-lactamase. Authors: Frohlich, C. / Bunzel, H.A. / Buda, K. / Mulholland, A.J. / van der Kamp, M.W. / Johnsen, P.J. / Leiros, H.S. / Tokuriki, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.7 KB | Display | ![]() |
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PDB format | ![]() | 147.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.1 KB | Display | ![]() |
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Full document | ![]() | 472.8 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8peaC ![]() 8pecC 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28002.713 Da / Num. of mol.: 1 / Mutation: A33V K51E F72L S212A T213A Source method: isolated from a genetically manipulated source Details: This is a mutant with these changes: A33V K51E F72L S212A T213A Source: (gene. exp.) ![]() ![]() ![]() Strain (production host): BL21AI harboring modified pURR expression References: UniProt: Q6XEC0, beta-lactamase |
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-Non-polymers , 5 types, 358 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-MLI / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1 M Tris, pH 9.0 (Sigma-Aldrich) 28-30% polyethylene glycol (PEG) mono ethylene ether 500 (Sigma-Aldrich) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→24.95 Å / Num. obs: 82172 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.11 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.041 / Rrim(I) all: 0.086 / Net I/av σ(I): 8.7 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.17→1.19 Å / Redundancy: 4 % / Rmerge(I) obs: 0.798 / Num. unique obs: 4063 / CC1/2: 0.521 / Rpim(I) all: 0.615 / Rrim(I) all: 1.244 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 23.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→24.95 Å
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Refine LS restraints |
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LS refinement shell |
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