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- PDB-5evk: Crystal structure of the metallo-beta-lactamase L1 in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5evk | ||||||
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Title | Crystal structure of the metallo-beta-lactamase L1 in complex with the bisthiazolidine inhibitor L-CS319 | ||||||
![]() | Metallo-beta-lactamase L1 | ||||||
![]() | HYDROLASE / inhibitor / carbapenemase / antibiotic resistance | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hinchliffe, P. / Spencer, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes. Authors: Hinchliffe, P. / Gonzalez, M.M. / Mojica, M.F. / Gonzalez, J.M. / Castillo, V. / Saiz, C. / Kosmopoulou, M. / Tooke, C.L. / Llarrull, L.I. / Mahler, G. / Bonomo, R.A. / Vila, A.J. / Spencer, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.1 KB | Display | ![]() |
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PDB format | ![]() | 95.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nq6C ![]() 5ev6C ![]() 5ev8C ![]() 5evbC ![]() 5evdC ![]() 5ew0C ![]() 5ewaC ![]() 1smlS S: Starting model for refinement 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
#1: Protein | Mass: 28894.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pOPIN-F / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-3C7 / ( | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.62 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 100 mM Hepes pH 7.75, 2.0 M ammonium sulphate, 1.5% PEG400. 1 ul protein (15 mg/ml) mixed with 1 ul reservoir. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.627→30.872 Å / Num. obs: 40522 / % possible obs: 99.69 % / Redundancy: 65.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 41.04 |
Reflection shell | Resolution: 1.627→1.66 Å / Redundancy: 27.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 6 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SML Resolution: 1.627→30.872 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.67 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.627→30.872 Å
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Refine LS restraints |
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LS refinement shell |
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