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- PDB-6p3v: 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: 6p3v | ||||||
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Title | Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT416 | ||||||
![]() | N-acetyltransferase Eis | ||||||
![]() | transferase/transferase inhibitor / Acetyltransferase / Aminoglycoside resistance / Competitive 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: Probing the Robustness of Inhibitors of Tuberculosis Aminoglycoside Resistance Enzyme Eis by Mutagenesis. Authors: Green, K.D. / Punetha, A. / Hou, C. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.2 KB | Display | ![]() |
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PDB format | ![]() | 69.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 708.3 KB | Display | ![]() |
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Full document | ![]() | 710.4 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p3tC ![]() 6p3uC ![]() 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
#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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#2: Chemical | ChemComp-NRV / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-DMS / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris-HCl pH 8.0 adjusted at room temperature, 10% 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 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 24278 / % possible obs: 97.9 % / Observed criterion σ(I): 2.1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.654 / Num. unique obs: 1210 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3R1K Resolution: 2.5→34.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.02 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→34.57 Å
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Refine LS restraints |
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