+Open data
-Basic information
Entry | Database: PDB / ID: 6kqx | ||||||
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Title | Crystal structure of Yijc from B. subtilis in complex with UDP | ||||||
Components | Uncharacterized UDP-glucosyltransferase YjiC | ||||||
Keywords | TRANSFERASE / prenyltransferase | ||||||
Function / homology | Function and homology information NDP-glycosyltransferase / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Hu, Y.M. / Dai, L.H. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Structural dissection of unnatural ginsenoside-biosynthetic UDP-glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate promiscuity. Authors: Dai, L.H. / Qin, L. / Hu, Y.M. / Huang, J.W. / Hu, Z. / Min, J. / Sun, Y. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kqx.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kqx.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kqx_validation.pdf.gz | 785.1 KB | Display | wwPDB validaton report |
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Full document | 6kqx_full_validation.pdf.gz | 800.1 KB | Display | |
Data in XML | 6kqx_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 6kqx_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/6kqx ftp://data.pdbj.org/pub/pdb/validation_reports/kq/6kqx | HTTPS FTP |
-Related structure data
Related structure data | 6kqwC 3iaaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44033.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: yjiC, BSU12220 / Plasmid: pET-46EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O34539, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-UDP / |
#3: 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: 3.2 Å3/Da / Density % sol: 61.57 % / Mosaicity: 1.602 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.2 M tri-Sodium Citrate dehydrate, 0.1 M Bis-Tris Propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 11, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→25 Å / Num. obs: 21112 / % possible obs: 98.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 56.83 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.029 / Rrim(I) all: 0.058 / Χ2: 1.46 / Net I/σ(I): 15 / Num. measured all: 83151 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IAA Resolution: 2.44→24.688 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.79 Å2 / Biso mean: 82.0275 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.44→24.688 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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