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- PDB-6tgi: Crystal structure of VIM-2 in complex with triazole-based inhibit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tgi | ||||||
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Title | Crystal structure of VIM-2 in complex with triazole-based inhibitor OP24 | ||||||
![]() | Vim-1 | ||||||
![]() | HYDROLASE / New Delhi metallo-beta-lactamase | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / membrane => GO:0016020 / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maso, L. / Spirakis, F. / Santucci, M. / Simon, C. / Docquier, J.D. / Cruciani, G. / Costi, M.P. / Tondi, D. / Cendron, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Virtual screening identifies broad-spectrum beta-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases. Authors: Spyrakis, F. / Santucci, M. / Maso, L. / Cross, S. / Gianquinto, E. / Sannio, F. / Verdirosa, F. / De Luca, F. / Docquier, J.D. / Cendron, L. / Tondi, D. / Venturelli, A. / Cruciani, G. / Costi, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.6 KB | Display | ![]() |
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PDB format | ![]() | 87.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tgdC ![]() 4bz3S 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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Unit cell |
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Components
#1: Protein | Mass: 26142.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Missing residues are present in the crystallized protein but not visible in the electron density maps. Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A485HTJ5, UniProt: Q9K2N0*PLUS, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FMT / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.25 M Magnesium Formate, 27 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39.56 Å / Num. obs: 54492 / % possible obs: 97.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5436 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BZ3 Resolution: 1.6→39.56 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.09 Å2 / Biso mean: 21.35 Å2 / Biso min: 9.36 Å2
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Refinement step | Cycle: final / Resolution: 1.6→39.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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