6Y6I

lipopolysaccharide outer core galactosyltransferase WaaB and UDP complex

• PDB DOI: https://doi.org/10.2210/pdb6Y6I/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-26 Released: 2021-03-31 
• Deposition Author(s): Zhang, Z.Y., Ashworth, G., Wang, Z.S., Zhu, X.F., Dong, C.J.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.213 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

Structural insights into the lipopolysaccharide outer core galactosyltransferase WaaB

Zhang, Z.Y., Ashworth, G., Wang, Z.S., Zhu, X.F., Dong, C.J.

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: 41.48 kDa 
• Atom Count: 3,200 
• Modelled Residue Count: 358 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipopolysaccharide 1,6-galactosyltransferase	A	361	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: rfaB, waaB, STM3719 EC: 2.4.1
UniProt
Find proteins for Q06994 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q06994  Go to UniProtKB:  Q06994

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.213 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.44	α = 90
b = 104.44	β = 90
c = 89.64	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Zhang, Z.Y., Ashworth, G., Wang, Z.S., Zhu, X.F., Dong, C.J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT106121MA

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description