8INJ | pdb_00008inj

Crystal structure of UGT74AN3-UDP-DIG

• PDB DOI: https://doi.org/10.2210/pdb8INJ/pdb

• Classification: TRANSFERASE
• Organism(s): Catharanthus roseus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-10 Released: 2024-02-14 
• Deposition Author(s): Feng, L., Wei, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UGT74AN3-UDP-DIG

Feng, L., Wei, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.58 kDa 
• Atom Count: 3,608 
• Modeled Residue Count: 426 
• Deposited Residue Count: 465 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	465	Catharanthus roseus	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for W8JMV4 (Catharanthus roseus) Explore W8JMV4  Go to UniProtKB:  W8JMV4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	B [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
DTX	C [auth A]	DIGITOXIGENIN C23 H34 O4 XZTUSOXSLKTKJQ-CESUGQOBSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.718	α = 90
b = 52.21	β = 90
c = 201.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Feng, L., Wei, H.

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

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release