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Yorodumi- PDB-8i09: Crystal structure of serine acetyltransferase from Salmonella typ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i09 | ||||||
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Title | Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with butyl gallate | ||||||
Components | Serine acetyltransferase | ||||||
Keywords | TRANSFERASE / SALMONELLA / SERINE ACETYLTRANSFERASE / CYSTEINE SYNTHESIS / BETA-HELIX | ||||||
Function / homology | Function and homology information serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Toyomoto, T. / Ono, K. / Shiba, T. / Momitani, K. / Zhang, T. / Tsutsuki, H. / Ishikawa, T. / Hoso, K. / Hamada, K. / Rahman, A. ...Toyomoto, T. / Ono, K. / Shiba, T. / Momitani, K. / Zhang, T. / Tsutsuki, H. / Ishikawa, T. / Hoso, K. / Hamada, K. / Rahman, A. / Zhong, H. / Akaike, T. / Yamamoto, K. / Matsuoka, M. / Hanaoka, K. / Niidome, T. / Sawa, T. | ||||||
Funding support | 1items
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Citation | Journal: Front Microbiol / Year: 2023 Title: Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics. Authors: Toyomoto, T. / Ono, K. / Shiba, T. / Momitani, K. / Zhang, T. / Tsutsuki, H. / Ishikawa, T. / Hoso, K. / Hamada, K. / Rahman, A. / Wen, L. / Maeda, Y. / Yamamoto, K. / Matsuoka, M. / ...Authors: Toyomoto, T. / Ono, K. / Shiba, T. / Momitani, K. / Zhang, T. / Tsutsuki, H. / Ishikawa, T. / Hoso, K. / Hamada, K. / Rahman, A. / Wen, L. / Maeda, Y. / Yamamoto, K. / Matsuoka, M. / Hanaoka, K. / Niidome, T. / Akaike, T. / Sawa, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i09.cif.gz | 564.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i09.ent.gz | 466.1 KB | Display | PDB format |
PDBx/mmJSON format | 8i09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i09_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 8i09_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 8i09_validation.xml.gz | 109.5 KB | Display | |
Data in CIF | 8i09_validation.cif.gz | 147.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/8i09 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/8i09 | HTTPS FTP |
-Related structure data
Related structure data | 8i04C 8i06C 7e3yS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30255.689 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: cysE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6I3Y9, serine O-acetyltransferase #2: Chemical | ChemComp-CYS / #3: Chemical | ChemComp-NF0 / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | 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: 2.13 Å3/Da / Density % sol: 42.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 MM HEPES, 100 MM SODIUM CHLORIDE, 15% MPD, 5 MM DTT, 5 MM butyl gallate PH range: 7.0-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2020 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 233218 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rpim(I) all: 0.102 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 38709 / CC1/2: 0.813 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7E3Y Resolution: 1.8→19.96 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.927 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.14 / 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: 38.969 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→19.96 Å
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Refine LS restraints |
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