6L8Z

Crystal structure of ugt transferase mutant in complex with UPG

PDB DOI: https://doi.org/10.2210/pdb6L8Z/pdb

Classification: TRANSFERASE
Organism(s): Siraitia grosvenorii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-07 Released: 2020-04-01
Deposition Author(s): Li, J., Shan, N., Yang, J.G., Liu, W.D., Sun, Y.X.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.266
R-Value Work: 0.212
R-Value Observed: 0.215

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Efficient O-Glycosylation of Triterpenes Enabled by Protein Engineering of Plant Glycosyltransferase UGT74AC1

Li, J., Yang, J.G., Mu, S., Shang, N., Liu, C., Zhu, Y., Cai, Y., Liu, P., Lin, J., Liu, W.D., Sun, Y.X., Ma, Y.

(2020) ACS Catal

DOI: https://doi.org/10.1021/acscatal.9b05232

Macromolecule Content

Total Structure Weight: 51.9 kDa
Atom Count: 3,621
Modelled Residue Count: 444
Deposited Residue Count: 454
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	454	Siraitia grosvenorii	Mutation(s): 0 Gene Names: UDPG1 EC: 2.4.1 (PDB Primary Data), 2.4.1.350 (UniProt)
UniProt
Find proteins for K7NBW3 (Siraitia grosvenorii) Explore K7NBW3 Go to UniProtKB: K7NBW3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K7NBW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG (Subject of Investigation/LOI) Query on UPG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.266
R-Value Work: 0.212
R-Value Observed: 0.215
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.311	α = 90
b = 69.153	β = 90
c = 141.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	--

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.