6SU6 | pdb_00006su6

Complex between a UDP-glucosyltransferase from Polygonum tinctorium capable of glucosylating indoxyl and UDP-glucose

PDB DOI: https://doi.org/10.2210/pdb6SU6/pdb

Classification: TRANSFERASE
Organism(s): Persicaria tinctoria
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-13 Released: 2020-09-30
Deposition Author(s): Fredslund, F., Teze, D., Svensson, B., Adams, P.D., Welner, D.H.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.263 (Depositor), 0.266 (DCC)
R-Value Work:
0.231 (Depositor), 0.234 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

O-/N-/S-Specificity in Glycosyltransferase Catalysis: From Mechanistic Understanding to Engineering

Teze, D., Coines, J., Fredslund, F., Dubey, K.D., Bidart, G.N., Adams, P.D., Dueber, J.E., Svensson, B., Rovira, C., Welner, D.H.

(2021) ACS Catal 11

DOI: https://doi.org/10.1021/acscatal.0c04171

Macromolecule Content

Total Structure Weight: 110.18 kDa
Atom Count: 7,274
Modeled Residue Count: 922
Deposited Residue Count: 998
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	499	Persicaria tinctoria	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for A0A2R2JFJ4 (Persicaria tinctoria) Explore A0A2R2JFJ4 Go to UniProtKB: A0A2R2JFJ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2R2JFJ4
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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.263 (Depositor), 0.266 (DCC)
R-Value Work: 0.231 (Depositor), 0.234 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.24	α = 90
b = 174.17	β = 90
c = 48.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17OC0025660
Novo Nordisk Foundation	Denmark	NNF10CC1016517

Revision History (Full details and data files)

Version 1.0: 2020-09-30
Type: Initial release
Version 1.1: 2021-04-21
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, 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.