8CGQ | pdb_00008cgq

Crystal structure of UGT708A6 with UDP

• PDB DOI: https://doi.org/10.2210/pdb8CGQ/pdb

• Classification: TRANSFERASE
• Organism(s): Zea mays
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-06 Released: 2024-02-21 
• Deposition Author(s): Fredslund, F., Bidart, G.N., Welner, D.H.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UGT708A6 with UDP

Fredslund, F., Bidart, G.N., Welner, D.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.16 kDa 
• Atom Count: 3,625 
• Modeled Residue Count: 458 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glycosyltransferase 708A6	A	476	Zea mays	Mutation(s): 0  Gene Names: UGT708A6 EC: 2.4.1
UniProt
Find proteins for A0A096SRM5 (Zea mays) Explore A0A096SRM5  Go to UniProtKB:  A0A096SRM5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	C [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
CL (Subject of Investigation/LOI)	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.431	α = 90
b = 72.593	β = 101.694
c = 57.018	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Fredslund, F., Bidart, G.N., Welner, D.H.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF20CC0035580

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release