+Open data
-Basic information
Entry | Database: PDB / ID: 7vm0 | |||||||||||||||
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Title | Crystal structure of YojK from B.subtilis in complex with UDP | |||||||||||||||
Components | Glycosyl transferase family 1 | |||||||||||||||
Keywords | TRANSFERASE / complex / dimer | |||||||||||||||
Function / homology | UDP-glycosyltransferase, MGT-like / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / hexosyltransferase activity / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase Function and homology information | |||||||||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||||||||
Authors | Hou, X.D. / Guo, B.D. / Rao, Y.J. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Front Bioeng Biotechnol / Year: 2022 Title: Highly efficient production of rebaudioside D enabled by structure-guided engineering of bacterial glycosyltransferase YojK. Authors: Guo, B. / Hou, X. / Zhang, Y. / Deng, Z. / Ping, Q. / Fu, K. / Yuan, Z. / Rao, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vm0.cif.gz | 173.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vm0.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vm0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7vm0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7vm0_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 7vm0_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/7vm0 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/7vm0 | HTTPS FTP |
-Related structure data
Related structure data | 6kqxS 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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Unit cell |
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-Components
#1: Protein | Mass: 46799.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yojK1, B4417_0117, CFD21_20150 / Production host: Escherichia coli (E. coli) / References: UniProt: L7V2W3 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | 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: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.09 M magnesium chloride, 0.09 M Tris-HCl, pH8.0, 25.2% (w/v) PEG3,350 and 0.05M sodium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 58223 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 0.955 / Net I/σ(I): 6 / Num. measured all: 401222 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KQX Resolution: 1.9→42.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.87 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.162 / 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: 87.69 Å2 / Biso mean: 22.986 Å2 / Biso min: 5.84 Å2
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Refinement step | Cycle: final / Resolution: 1.9→42.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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