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- PDB-4oqg: Crystal structure of TEM-1 beta-lactamase in complex with boron-b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4oqg | ||||||
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Title | Crystal structure of TEM-1 beta-lactamase in complex with boron-based inhibitor EC25 | ||||||
![]() | Ampicillin resistance protein | ||||||
![]() | hydrolase/hydrolase inhibitor / Beta-lactamase / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic 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 | ![]() | 306 KB | Display | ![]() |
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PDB format | ![]() | 251.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 56.8 KB | Display | |
Data in CIF | ![]() | 75.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4op5C ![]() 4op8C ![]() 4opqC ![]() 4oprC ![]() 4opyC ![]() 4opzC ![]() 4oq0C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 28984.076 Da / Num. of mol.: 6 / Fragment: TEM-1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-2UL / #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, 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: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82658 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.81 Å / Num. obs: 65358 / % possible obs: 96.4 % / Observed criterion σ(I): 3 / Redundancy: 5.06 % / Rsym value: 0.071 / Net I/σ(I): 14.64 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4.66 % / Mean I/σ(I) obs: 3 / Rsym value: 0.539 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZG4 Resolution: 2.4→45.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.976 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.291 / 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: 52.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→45.81 Å
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Refine LS restraints |
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