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- PDB-4oq0: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4oq0 | ||||||
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Title | Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutation in complex with boron-based inhibitor EC25 | ||||||
![]() | TEM-94 ES-beta-lactamase | ||||||
![]() | hydrolase/hydrolase inhibitor / Beta-lactamase / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dellus-Gur, E. / Elias, M. / Fraser, J.S. / Tawfik, D.S. | ||||||
![]() | ![]() Title: Negative Epistasis and Evolvability in TEM-1 beta-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder. Authors: Dellus-Gur, E. / Elias, M. / Caselli, E. / Prati, F. / Salverda, M.L. / de Visser, J.A. / Fraser, J.S. / Tawfik, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.3 KB | Display | ![]() |
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PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 819.1 KB | Display | ![]() |
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Full document | ![]() | 825.6 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4op5C ![]() 4op8C ![]() 4opqC ![]() 4oprC ![]() 4opyC ![]() 4opzC ![]() 4oqgC ![]() 4oqhC ![]() 4oqiC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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: 28730.689 Da / Num. of mol.: 1 / Fragment: TEM-1 Mutation: G238S, R164S, A42G, N52A, I84V, R120G, M182T, L201A, T265M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 287 molecules ![](data/chem/img/2UL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-2UL / |
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#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-PEG / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | Temperature: 293 K / pH: 6.2 Details: 9% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES, and 200mM Ca(OAc)2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→26.2 Å / Num. obs: 42706 / Observed criterion σ(I): 3 / Rsym value: 0.038 / Net I/σ(I): 27.63 |
Reflection shell | Resolution: 1.42→1.6 Å / Redundancy: 5.62 % / Mean I/σ(I) obs: 10.86 / Rsym value: 0.14 / % possible all: 89.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 16.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→26.2 Å
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Refine LS restraints |
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