8YP7 | pdb_00008yp7

Crystal structure of glucosyltransferase RrUGT3

PDB DOI: https://doi.org/10.2210/pdb8YP7/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Rhodiola rosea
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-15 Released: 2025-03-19
Deposition Author(s): Cai, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.212 (Depositor), 0.219 (DCC)
R-Value Work:
0.179 (Depositor), 0.188 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8YP7

This is version 1.1 of the entry. See complete history.

Literature

Reaction mechanism and regioselectivity of uridine diphosphate glucosyltransferase RrUGT3: a combined experimental and computational study

Li, M., You, C., Guo, F., Han, Q., Xie, X., Ma, L., Li, S., Du, L., Sheng, X., Su, H.

(2024) Catal Sci Technol 14: 4882-4895

DOI: https://doi.org/10.1039/d4cy00721b

Macromolecule Content

Total Structure Weight: 52.09 kDa
Atom Count: 3,579
Modeled Residue Count: 445
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	474	Rhodiola rosea	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for A0A2I6B3N5 (Rhodiola rosea) Explore A0A2I6B3N5 Go to UniProtKB: A0A2I6B3N5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2I6B3N5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.212 (Depositor), 0.219 (DCC)
R-Value Work: 0.179 (Depositor), 0.188 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.191	α = 90
b = 70.826	β = 90
c = 92.662	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200030

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release
Version 1.1: 2026-10-14
Changes: Database references