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- PDB-6vv3: Crystal structure of Eis from Mycobacterium tuberculosis in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vv3 | ||||||
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Title | Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT1358 | ||||||
![]() | N-acetyltransferase Eis | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Acetyltransferase / Resistance / Aminoglycoside / Competitive / 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. / Hou, C. / Ngo, H.X. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis fromMycobacterium tuberculosis. Authors: Punetha, A. / Ngo, H.X. / Holbrook, S.Y.L. / Green, K.D. / Willby, M.J. / Bonnett, S.A. / Krieger, K. / Dennis, E.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 | ![]() | 100.8 KB | Display | ![]() |
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PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6vurC ![]() 6vusC ![]() 6vutC ![]() 6vuuC ![]() 6vuwC ![]() 6vuxC ![]() 6vuyC ![]() 6vuzC ![]() 6vv0C ![]() 6vv1C ![]() 6vv2C ![]() 3r1kS 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 A
#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, 245 molecules ![](data/chem/img/RM7.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-RM7 / | ||||||
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#3: Chemical | ChemComp-DMS / | ||||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | #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: 4.03 Å3/Da / Density % sol: 69.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris-HCl pH 8.0 adjusted at room temperature, 7% w/v PEG 8000, and 400 mM (NH4)2SO4 |
-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, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 28642 / % possible obs: 98.9 % / Redundancy: 6.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 1.132 / Num. unique obs: 1444 / CC1/2: 0.813 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3R1K Resolution: 2.4→35 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.197 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 123.58 Å2 / Biso mean: 42.213 Å2 / Biso min: 23.75 Å2
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Refinement step | Cycle: final / Resolution: 2.4→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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