+Open data
-Basic information
Entry | Database: PDB / ID: 3uy5 | ||||||
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Title | crystal structure of Eis from Mycobacterium tuberculosis | ||||||
Components | Enhanced intracellular survival protein | ||||||
Keywords | TRANSFERASE / GNAT fold / acetyl transferase | ||||||
Function / homology | Function and homology information effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host programmed cell death / 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 / bacterial extracellular vesicle / biological process involved in interaction with host ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host programmed cell death / 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 / 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kim, K.H. / Suh, S.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Mycobacterium tuberculosis Eis protein initiates suppression of host immune responses by acetylation of DUSP16/MKP-7 Authors: Kim, K.H. / An, D.R. / Song, J. / Yoon, J.Y. / Kim, H.S. / Yoon, H.J. / Im, H.N. / Kim, J. / Kim, D.J. / Lee, S.J. / Kim, K.H. / Lee, H.M. / Kim, H.J. / Jo, E.K. / Lee, J.Y. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uy5.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uy5.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 3uy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/3uy5 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/3uy5 | HTTPS FTP |
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-Related structure data
-Links
-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
#1: Protein | Mass: 46644.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: eis, MT2489, MTCY253.04, Rv2416c / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS(DE3) / References: UniProt: P71727, UniProt: P9WFK7*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 300mM ammonium citrate, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→20 Å / Num. obs: 26334 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.841 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 0 / Phase error: 20.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.409 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.82 Å2 / Biso mean: 32.7382 Å2 / Biso min: 12.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.841 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: 9
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