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Yorodumi- PDB-8fkl: Truncated form of the catalytic domain of Streptococcus mutans GtfB -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fkl | ||||||
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Title | Truncated form of the catalytic domain of Streptococcus mutans GtfB | ||||||
Components | Glucosyltransferase-I | ||||||
Keywords | TRANSFERASE / GtfB (GTF-I) / biofilm / streptococcus mutans / insoluble 1 / 3-linked alpha glucans / 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: 1.48 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 | 8fkl.cif.gz | 234.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fkl.ent.gz | 185.2 KB | Display | PDB format |
PDBx/mmJSON format | 8fkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/8fkl ftp://data.pdbj.org/pub/pdb/validation_reports/fk/8fkl | HTTPS FTP |
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-Related structure data
Related structure data | 8fj9C 8fjcC 8fk4C 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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Unit cell |
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-Components
#1: Protein | Mass: 57593.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Constitutes a truncated (proteolysed) version of the catalytic domain of Streptococcus mutans at high resolution. 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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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61 % / Description: block-like |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% PEG 8000, 0.2 M magnesium chloride, 0.1 M Caps |
-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: Dec 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→92.26 Å / Num. obs: 121563 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Χ2: 0.98 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 7 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5970 / CC1/2: 0.861 / CC star: 0.925 / Rpim(I) all: 0.255 / Rrim(I) all: 0.677 / Χ2: 0.82 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→64.74 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.029 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 103.75 Å2 / Biso mean: 27.777 Å2 / Biso min: 14.72 Å2
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Refinement step | Cycle: final / Resolution: 1.48→64.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.518 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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