+Open data
-Basic information
Entry | Database: PDB / ID: 8h5d | ||||||
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Title | Crystal structure of YojK mutant in complex with UDP | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / Glycosyltransferase / Rebaudioside D / Complex | ||||||
Function / homology | UDP-glycosyltransferase, MGT-like / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / hexosyltransferase activity / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / Uncharacterized UDP-glucosyltransferase YojK Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Hou, X.D. / Yang, S. / Yin, D.J. / Rao, Y.J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Improving the Thermostability of Glycosyltransferase YojK by Targeting Mutagenesis for Highly Efficient Biosynthesis of Rebaudioside D Authors: Yang, S. / Hou, X.D. / Deng, Z.W. / Yang, L.F. / Ping, Q. / Yuan, Z.B. / Zhang, Y. / Rao, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h5d.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h5d.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 8h5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h5d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8h5d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8h5d_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 8h5d_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/8h5d ftp://data.pdbj.org/pub/pdb/validation_reports/h5/8h5d | HTTPS FTP |
-Related structure data
Related structure data | 7vm0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47012.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O31853 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 1.97 Å3/Da / Density % sol: 37.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Ammonium acetate, 0.1 M HEPES (pH 7.5) and 25% (w/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Sep 2, 2022 | ||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.498→62.35 Å / Num. obs: 25482 / % possible obs: 99.76 % / Redundancy: 9.51 % / Rsym value: 0.277 / Net I/av σ(I): 23.203 / Net I/σ(I): 12.8 | ||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VM0 Resolution: 2.5→62.35 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.642 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.361 / 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: 116.7 Å2 / Biso mean: 30.116 Å2 / Biso min: 4.75 Å2
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Refinement step | Cycle: final / Resolution: 2.5→62.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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