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- PDB-5ev8: Crystal structure of the metallo-beta-lactamase IMP-1 in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ev8 | ||||||
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Title | Crystal structure of the metallo-beta-lactamase IMP-1 in complex with the bisthiazolidine inhibitor D-CS319 | ||||||
![]() | Beta-lactamase IMP-1 | ||||||
![]() | HYDROLASE / inhibitor / carbapenemase / antibiotic resistance | ||||||
Function / homology | ![]() 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 | ![]() | 193.3 KB | Display | ![]() |
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PDB format | ![]() | 152.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499.9 KB | Display | ![]() |
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Full document | ![]() | 514.7 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 50.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nq6C ![]() 5ev6C ![]() 5evbC ![]() 5evdC ![]() 5evkC ![]() 5ew0C ![]() 5ewaC ![]() 1ddkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 25300.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 309 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/3R9.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/3R9.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-3R9 / ( #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium acetate, 25% PEG 8000. 1ul protein (25 mg/ml) mixed with 1ul reagent |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→37.24 Å / Num. obs: 45125 / % possible obs: 100 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 18.1 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DDK Resolution: 2.3→37.238 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.81 / 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: 2.3→37.238 Å
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Refine LS restraints |
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LS refinement shell |
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