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- PDB-6x7a: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x7a | ||||||
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Title | Crystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with inhibitor SGT572 | ||||||
![]() | N-acetyltransferase Eis | ||||||
![]() | TRANSFERASE/TRANSFERASE Inhibitor / Aminoglycoside / Drug resistance / Repurposing / Acetylation / Inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex | ||||||
Function / homology | ![]() effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / biological process involved in interaction with host ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / biological process involved in interaction with host / host cell cytoplasmic vesicle / N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / host extracellular space / response to antibiotic / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Punetha, A. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based design of haloperidol analogues as inhibitors of acetyltransferase Eis from Mycobacterium tuberculosis to overcome kanamycin resistance Authors: Punetha, A. / Green, K.D. / Garzan, A. / Willby, M.J. / Pang, A.H. / Hou, C. / Holbrook, S.Y.L. / Krieger, K. / Posey, J.E. / Parish, T. / Tsodikov, O.V. / Garneau-Tsodikova, 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 | ![]() | 107.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 686.9 KB | Display | ![]() |
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Full document | ![]() | 688.8 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x10SC ![]() 6x6gC ![]() 6x6iC ![]() 6x6yC 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 45999.113 Da / Num. of mol.: 1 / Mutation: C204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: eis, Rv2416c, MTCY253.04 / Production host: ![]() ![]() References: UniProt: P9WFK7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-Non-polymers , 6 types, 359 molecules ![](data/chem/img/UTD.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UTD / | ||||||
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#3: Chemical | ChemComp-PEG / | ||||||
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl pH 8.5, 13% PEG 8000 and 0.4 M (NH4)2SO4, 5 mM kanamycin, 4 mM CoA. Kanamycin, CoA and (NH4)2SO4 were replaced by 0.5 mM inhibitor on soaking. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 43424 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 2.08→2.12 Å / Rmerge(I) obs: 0.77 / Num. unique obs: 2160 / CC1/2: 0.85 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6X10 Resolution: 2.08→40.003 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.16 / SU B: 3.678 / SU ML: 0.093 / Average fsc free: 0.9263 / Average fsc work: 0.9291 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.118 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.775 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→40.003 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: 20
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