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Yorodumi- PDB-3sxo: Mycobacterium tuberculosis Eis protein initiates modulation of ho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sxo | ||||||
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Title | Mycobacterium tuberculosis Eis protein initiates modulation of host immune responses by acetylation of DUSP16/MKP-7 | ||||||
Components | Enhanced intracellular survival protein | ||||||
Keywords | TRANSFERASE / GNAT fold / acetyltransferase / acetyl CoA binding | ||||||
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. / An, D.R. / Yoon, J.Y. / Kim, H.S. / Yoon, H.J. / Song, J.S. / Im, H.N. / Kim, J. / Kim, D.J. / Lee, S.J. ...Kim, K.H. / An, D.R. / Yoon, J.Y. / Kim, H.S. / Yoon, H.J. / Song, J.S. / Im, H.N. / Kim, J. / Kim, D.J. / Lee, S.J. / Kim, H.J. / Lee, J.Y. / Suh, S.W. | ||||||
Citation | Journal: To be Published Title: Mycobacterium tuberculosis Eis protein initiates modulation of host immune responses by acetylation of DUSP16/MKP-7 Authors: Kim, K.H. / An, D.R. / Yoon, J.Y. / Kim, H.S. / Yoon, H.J. / Song, J.S. / Im, H.N. / Kim, J. / Kim, D.J. / Lee, S.J. / Kim, H.J. / 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 | 3sxo.cif.gz | 168.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sxo.ent.gz | 134 KB | Display | PDB format |
PDBx/mmJSON format | 3sxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sxo ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sxo | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46644.797 Da / Num. of mol.: 2 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) / References: UniProt: P71727, UniProt: P9WFK7*PLUS #2: Water | ChemComp-HOH / | |
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-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: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12% PEG 3350, 300mM Ammonium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-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 / Date: Jan 24, 2010 |
Radiation | Monochromator: Si PIN photodiode detector / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→30 Å / Num. obs: 50998 / % possible obs: 99.9 % / Biso Wilson estimate: 30.71 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 34.3 |
Reflection shell | Resolution: 2.46→2.55 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 5.41 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.841 Å / SU ML: 0.68 / σ(F): 1.97 / Phase error: 21.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.936 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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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 |
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