3RU9 | pdb_00003ru9

Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase

• PDB DOI: https://doi.org/10.2210/pdb3RU9/pdb

• Classification: ISOMERASE
• Organism(s): Plesiomonas shigelloides
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-04 Released: 2011-05-25 
• Deposition Author(s): Bhatt, V.S., Guan, W., Wang, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase

Bhatt, V.S., Guan, W., Wang, P.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.28 kDa 
• Atom Count: 11,333 
• Modeled Residue Count: 1,344 
• Deposited Residue Count: 1,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WbgU	A, B, C, D	351	Plesiomonas shigelloides	Mutation(s): 0  Gene Names: wbgU EC: 5.1.3.7
UniProt
Find proteins for Q7BJX9 (Plesiomonas shigelloides) Explore Q7BJX9  Go to UniProtKB:  Q7BJX9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], I [auth B], L [auth C], O [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	F [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GLY	K [auth C], N [auth D]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
UNL	G [auth A], J [auth B], M [auth C], P [auth D]	Unknown ligand DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.41	α = 90
b = 77.41	β = 90
c = 224.887	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Bhatt, V.S., Guan, W., Wang, P.G.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description