5N80 | pdb_00005n80

glycosyltransferase LPS biosynthesis in complex with UDP

• PDB DOI: https://doi.org/10.2210/pdb5N80/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-02-21 Released: 2018-03-14 
• Deposition Author(s): Zhang, Z., Ashworth, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.271 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

glycosyltransferase LPS biosynthesis in complex with UDP

Zhang, Z., Ashworth, G.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.42 kDa 
• Atom Count: 2,955 
• Modeled Residue Count: 358 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipopolysaccharide 1,6-galactosyltransferase	A	360	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	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:  0.271 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

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
PHENIX	refinement
xia2	data collection
xia2	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Zhang, Z., Ashworth, G.J.

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 2.0: 2018-04-25
  Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 3.0: 2019-06-12
  Changes: Atomic model, Data collection, Database references, Structure summary
• Version 3.1: 2019-10-16
  Changes: Data collection
• Version 3.2: 2024-05-08
  Changes: Data collection, Database references