8H5D

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 
• R-Value Work: 0.179 
• R-Value Observed: 0.183 

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.

To be published.

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 
• Modelled 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
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 
• R-Value Work: 0.179 
• R-Value Observed: 0.183 
• 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