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Yorodumi- PDB-8fjc: Structure of the catalytic domain of Streptococcus mutans GtfB co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fjc | ||||||
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Title | Structure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in tetragonal space group P4322 | ||||||
Components | Glucosyltransferase-I | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / GtfB / GTF-I / insoluble 1 / 3-linked alpha Glucans / Biofilm / Glucansucrase / inhibitor Acarbose / TRANSFERASE / TRANSFERASE-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: 2.5 Å | ||||||
Authors | Schormann, N. / Deivanayagam, C. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis. Authors: Schormann, N. / Patel, M. / Thannickal, L. / Purushotham, S. / Wu, R. / Mieher, J.L. / Wu, H. / Deivanayagam, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fjc.cif.gz | 360.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fjc.ent.gz | 284 KB | Display | PDB format |
PDBx/mmJSON format | 8fjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fjc_validation.pdf.gz | 17 MB | Display | wwPDB validaton report |
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Full document | 8fjc_full_validation.pdf.gz | 17 MB | Display | |
Data in XML | 8fjc_validation.xml.gz | 60.2 KB | Display | |
Data in CIF | 8fjc_validation.cif.gz | 86.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/8fjc ftp://data.pdbj.org/pub/pdb/validation_reports/fj/8fjc | HTTPS FTP |
-Related structure data
Related structure data | 8fj9C 8fk4C 8fklC 8fn5C 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 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 #2: Polysaccharide | |
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-Non-polymers , 4 types, 384 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #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: 4.34 Å3/Da / Density % sol: 71.69 % |
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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; tetragonal apo crystals were soaked with acarbose at a 1:10 molar ratio for 5-10 mins (stock solution of 100 mM in water; final concentration 1-2 mM) |
-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: Jun 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→86.72 Å / Num. obs: 119150 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 41.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.084 / Rrim(I) all: 0.266 / Χ2: 1 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5822 / CC1/2: 0.446 / CC star: 0.785 / Rpim(I) all: 0.595 / Χ2: 0.97 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→83.715 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→83.715 Å
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Refine LS restraints |
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LS refinement shell |
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