Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content

• Total Structure Weight: 651.05 kDa 
• Atom Count: 42916 
• Residue Count: 5520 
• Unique protein chains: 1

3GND

Crystal Structure of E. coli LsrF in complex with Ribulose-5-phosphate

• DOI: 10.2210/pdb3GND/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-17 Released: 2009-09-08 
• Deposition Author(s): Miller, S.T., Diaz, Z.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.

Diaz, Z., Xavier, K.B., Miller, S.T.

(2009) PLoS One 4: e6820-e6820

• PubMed: 19714241 
• DOI: 10.1371/journal.pone.0006820
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (alphabeta)(8)-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology with aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aldolase lsrF	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	295	Escherichia coli K-12	Mutation(s): 0  Gene Names: b1517, JW1510, lsrF, yneB EC: 4.1.2 (PDB Primary Data), 2.3.1.245 (UniProt)
Find proteins for P76143 (Escherichia coli (strain K12)) Go to UniProtKB:  P76143

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5RP	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	RIBULOSE-5-PHOSPHATE C5 H11 O8 P FNZLKVNUWIIPSJ-UHNVWZDZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.741	α = 90
b = 107.102	β = 102.62
c = 169.516	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-17 
• Released Date: 2009-09-08 
Deposition Author(s): Miller, S.T., Diaz, Z.C.

Revision History 

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description