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Yorodumi- PDB-8fj9: Structure of the catalytic domain of Streptococcus mutans GtfB in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fj9 | ||||||
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Title | Structure of the catalytic domain of Streptococcus mutans GtfB in tetragonal space group P4322 | ||||||
Components | Glucosyltransferase-I | ||||||
Keywords | TRANSFERASE / GtfB / GTF-I / insoluble 1 / 3-linked alpha Glucans / Biofilm / Glucansucrase | ||||||
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 | 8fj9.cif.gz | 354.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fj9.ent.gz | 278.6 KB | Display | PDB format |
PDBx/mmJSON format | 8fj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/8fj9 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/8fj9 | HTTPS FTP |
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-Related structure data
Related structure data | 8fjcC 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 , 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, 405 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #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: 4.37 Å3/Da / Density % sol: 71.88 % |
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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 |
-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→86.92 Å / Num. obs: 119867 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.314 / Rpim(I) all: 0.072 / Rrim(I) all: 0.322 / Χ2: 1.01 / Net I/σ(I): 9.3 / Num. measured all: 2410102 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 21 % / Num. unique obs: 5852 / CC1/2: 0.439 / CC star: 0.781 / Rpim(I) all: 0.882 / Χ2: 0.99 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→75.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.165 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.213 / 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: 54.917 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→75.7 Å
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Refine LS restraints |
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