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Yorodumi- PDB-8f55: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f55 | ||||||
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Title | Crystal structure of acetyltransferase Eis from Mycobacterium tuberculosis H37Rv in complex with inhibitor SGT1614 | ||||||
Components | N-acetyltransferase Eis | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / drug resistance / acetylation / histone / inhibition / aminoglycoside / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Pang, A.H. / Punetha, A. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Discovery and Mechanistic Analysis of Structurally Diverse Inhibitors of Acetyltransferase Eis among FDA-Approved Drugs. Authors: Pang, A.H. / Green, K.D. / Punetha, A. / Thamban Chandrika, N. / Howard, K.C. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f55.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f55.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 8f55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f55_validation.pdf.gz | 679.4 KB | Display | wwPDB validaton report |
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Full document | 8f55_full_validation.pdf.gz | 682.1 KB | Display | |
Data in XML | 8f55_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 8f55_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/8f55 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/8f55 | HTTPS FTP |
-Related structure data
Related structure data | 8f4aC 8f4tC 8f4uC 8f4wC 8f4zC 8f51C 8f57C 8f58C 3r1kS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-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.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: eis, Rv2416c, MTCY253.04 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WFK7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | ChemComp-XF2 / ( | ||||||
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#3: Chemical | ChemComp-DMS / #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 4.24 Å3/Da / Density % sol: 71.02 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: Tris-HCl pH 8.5 (0.1 M), PEG 8000 (10% w/v), and (NH4)2SO4 (0.5 M) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 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: 2.15→50 Å / Num. obs: 39231 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.15→2.19 Å / Num. unique obs: 1961 / CC1/2: 0.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R1K Resolution: 2.2→37.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.188 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.158 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→37.27 Å
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