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- PDB-8d25: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d25 | ||||||
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Title | Crystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with inhibitor SGT530 | ||||||
![]() | N-acetyltransferase Eis | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / resistance / aminoglycoside / enzyme / inhibitor / acetyl transfer / 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 | ![]() ![]() ![]() | ||||||
![]() | Pang, A.H. / Punetha, A. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of substituted benzyloxy-benzylamine inhibitors of acetyltransferase Eis and their anti-mycobacterial activity. Authors: Pang, A.H. / Green, K.D. / Chandrika, N.T. / Garzan, A. / Punetha, A. / Holbrook, S.Y.L. / Willby, M.J. / Posey, J.E. / 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 | ![]() | 97.6 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8d1rC ![]() 8d23C ![]() 3r1kS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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-PV3 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris-HCl pH 8.5, 9.5-10% w/v PEG 8000, and 500 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: Jun 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 44989 / % possible obs: 99.4 % / Observed criterion σ(I): 2.1 / Redundancy: 7.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.05→2.09 Å / Rmerge(I) obs: 0.618 / Num. unique obs: 2230 / CC1/2: 0.893 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3R1K Resolution: 2.05→42.03 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.27 Å2 / Biso mean: 31.516 Å2 / Biso min: 18.04 Å2
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Refinement step | Cycle: final / Resolution: 2.05→42.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.051→2.104 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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