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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.273 (Depositor), 0.274 (DCC)
R-Value Work:
0.179 (Depositor), 0.187 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31853
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.273 (Depositor), 0.274 (DCC)
R-Value Work: 0.179 (Depositor), 0.187 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	China	--

Revision History (Full details and data files)

Version 1.0: 2023-10-18
Type: Initial release
Version 1.1: 2025-04-30
Changes: Database references, Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.