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- PDB-5lcf: VIM-2 metallo-beta-lactamase in complex with 3-oxo-2-phenylisoind... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lcf | ||||||
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Title | VIM-2 metallo-beta-lactamase in complex with 3-oxo-2-phenylisoindoline-4-carboxylic acid (compound 30) | ||||||
![]() | Metallo-beta-lactamase VIM-2 | ||||||
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Function / homology | ![]() antibiotic catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, G.-B. / Brem, J. / McDonough, M.A. / Schofield, C.J. | ||||||
![]() | ![]() Title: NMR-filtered virtual screening leads to non-metal chelating metallo-beta-lactamase inhibitors. Authors: Li, G.B. / Abboud, M.I. / Brem, J. / Someya, H. / Lohans, C.T. / Yang, S.Y. / Spencer, J. / Wareham, D.W. / McDonough, M.A. / Schofield, C.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 | ![]() | 105.5 KB | Display | ![]() |
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PDB format | ![]() | 78.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lcaC ![]() 5lchC ![]() 5le1C ![]() 5lm6C ![]() 4c1dS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28352.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 Plasmid: OPINF / Details (production host): PLASMID DERIVED NON-GENOMIC / Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 253 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/6TJ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/6TJ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-6TJ / | #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.7 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Magnesium Formate, 21% (v/v) Polyethylene glycol 3350, 5 mM 3-oxo-2-phenylisoindoline-4-carboxylic acid, 16 mg/mL protein |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 13, 2016 / Details: OSMIC HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→50 Å / Num. obs: 16377 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.94 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Χ2: 1.06 / Net I/av σ(I): 26.418 / Net I/σ(I): 18.2 / Num. measured all: 110191 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4C1D Resolution: 1.86→24.055 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.86 Å2 / Biso mean: 15.2723 Å2 / Biso min: 5.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.86→24.055 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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