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Yorodumi- PDB-8fg8: Catalytic domain of GtfB in complex with inhibitor 2-[(2,4,5-Trih... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fg8 | ||||||
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Title | Catalytic domain of GtfB in complex with inhibitor 2-[(2,4,5-Trihydroxyphenyl)methylidene]-1-benzofuran-3-one | ||||||
Components | Glucosyltransferase-I | ||||||
Keywords | TRANSFERASE/INHIBITOR / GtfB / GTF-I / catalytic domain / inhibitor / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / extracellular region Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Schormann, N. / Deivanayagam, C. / Velu, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Hydrogel-Encapsulated Biofilm Inhibitors Abrogate the Cariogenic Activity of Streptococcus mutans . Authors: Ahirwar, P. / Kozlovskaya, V. / Nijampatnam, B. / Rojas, E.M. / Pukkanasut, P. / Inman, D. / Dolmat, M. / Law, A.C. / Schormann, N. / Deivanayagam, C. / Harber, G.J. / Michalek, S.M. / Wu, H. ...Authors: Ahirwar, P. / Kozlovskaya, V. / Nijampatnam, B. / Rojas, E.M. / Pukkanasut, P. / Inman, D. / Dolmat, M. / Law, A.C. / Schormann, N. / Deivanayagam, C. / Harber, G.J. / Michalek, S.M. / Wu, H. / Kharlampieva, E. / Velu, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fg8.cif.gz | 357.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fg8.ent.gz | 280.1 KB | Display | PDB format |
PDBx/mmJSON format | 8fg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/8fg8 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/8fg8 | HTTPS FTP |
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-Related structure data
Related structure data | 3aieS S: Starting model for refinement |
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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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 97510.484 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 191-1051) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: gtfB, SMU_1004 / Plasmid: pET-23d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08987, dextransucrase |
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-Non-polymers , 5 types, 534 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-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: 4.42 Å3/Da / Density % sol: 72.2 % / Description: Tetragonal rods |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2 M ammonium sulfate, 0.1 M Bis-Tris, apo- crystals soaked 5-10 mins with inhibitor HA5 (20 mM aqueous stock solution; 1-2 mM final concentration) |
-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 EIGER2 S 16M / Detector: PIXEL / Date: Aug 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→87.25 Å / Num. obs: 142674 / % possible obs: 98.5 % / Redundancy: 9.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.065 / Rrim(I) all: 0.202 / Χ2: 0.98 / Net I/σ(I): 8.1 / Num. measured all: 1293084 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 9.3 % / Num. unique obs: 7062 / CC1/2: 0.35 / Rpim(I) all: 0.712 / Χ2: 0.89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3AIE Resolution: 2.35→73.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.384 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.181 / 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: 57.9 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→73.04 Å
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