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- PDB-4opz: 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: 4opz | ||||||
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Title | Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying 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 | ![]() | 144 KB | Display | ![]() |
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PDB format | ![]() | 111.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 824.1 KB | Display | ![]() |
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Full document | ![]() | 826.4 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4op5C ![]() 4op8C ![]() 4opqC ![]() 4oprC ![]() 4opyC ![]() 4oq0C ![]() 4oqgC ![]() 4oqhC ![]() 4oqiC ![]() 1zg4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 28800.807 Da / Num. of mol.: 1 / Fragment: TEM-1 Mutation: G238S, 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, 383 molecules ![](data/chem/img/2UL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.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-ACT / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.11 % |
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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: 1.45→31.15 Å / Num. obs: 43208 / Observed criterion σ(I): 3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1ZG4 Resolution: 1.45→31.17 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.236 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 15.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→31.17 Å
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Refine LS restraints |
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