7XRE

Crystal structure of DgpA

• PDB DOI: https://doi.org/10.2210/pdb7XRE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): human intestinal bacterium PUE
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-05-10 Released: 2023-02-15 
• Deposition Author(s): Ma, W., He, P.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.294 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 

Literature

Structural mechanism of a dual-functional enzyme DgpA/B/C as both a C-glycoside cleaving enzyme and an O- to C-glycoside isomerase.

He, P., Wang, S., Li, S., Liu, S., Zhou, S., Wang, J., Tao, J., Wang, D., Wang, R., Ma, W.

(2023) Acta Pharm Sin B 13: 246-255

• DOI: https://doi.org/10.1016/j.apsb.2022.05.022

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 247.61 kDa 
• Atom Count: 16,550 
• Modelled Residue Count: 2,151 
• Deposited Residue Count: 2,202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DgpA	A, B, C, D, E, F	367	human intestinal bacterium PUE	Mutation(s): 0  Gene Names: dgpA
UniProt
Find proteins for A0A3Q9WWX8 (human intestinal bacterium PUE) Explore A0A3Q9WWX8  Go to UniProtKB:  A0A3Q9WWX8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.294 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.79	α = 90
b = 130.76	β = 90
c = 206.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Ma, W., He, P.

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Funding Organization	Location	Grant Number
Other government	China	90011451310011
Other government	China	1000061223476

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release