8H5D | pdb_00008h5d

Crystal structure of YojK mutant in complex with UDP

• PDB DOI: https://doi.org/10.2210/pdb8H5D/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-10-12 Released: 2023-10-18 
• Deposition Author(s): Hou, X.D., Yang, S., Yin, D.J., Rao, Y.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Improving the thermostability of glycosyltransferase YojK by targeting mutagenesis for highly efficient biosynthesis of rebaudioside D.

Yang, S., Hou, X.D., Deng, Z.W., Yang, L.F., Ping, Q., Yuan, Z.B., Zhang, Y., Rao, Y.J.

(2023) Mol Catal 535

• DOI: https://doi.org/10.1016/j.mcat.2022.112898

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.92 kDa 
• Atom Count: 6,525 
• Modeled Residue Count: 781 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	414	Bacillus subtilis	Mutation(s): 5  EC: 2.4.1
UniProt
Find proteins for O31853 (Bacillus subtilis (strain 168)) Explore O31853  Go to UniProtKB:  O31853

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	C [auth A], E [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.753	α = 90
b = 79.979	β = 91.1
c = 99.244	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Hou, X.D., Yang, S., Yin, D.J., Rao, Y.J.

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Funding Organization	Location	Grant Number
Other private	China	--

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2025-04-30
  Changes: Database references, Structure summary