5GTA | pdb_00005gta

3D Crystal Structure of LsrB Bound to Furanosyl diester (R)-THMF, from Salmonella typhi

• PDB DOI: https://doi.org/10.2210/pdb5GTA/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-19 Released: 2017-08-23 
• Deposition Author(s): Gopinath, S., Perumal, P., Rahul, R., Arockiasamy, A., SundaraBaalaji, N.
• Funding Organization(s): Indian Council of Medical Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

3D Crystal Structure of LsrB Bound to Furanosyl diester (R)-THMF, from Salmonella typhi

Gopinath, S., Perumal, P., Rahul, R., Arockiasamy, A., Sundarabaalaji, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.97 kDa 
• Atom Count: 2,417 
• Modeled Residue Count: 314 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autoinducer 2-binding protein LsrB	A	340	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  Gene Names: lsrB, STY3793, t3541
UniProt
Find proteins for Q8Z2X8 (Salmonella typhi) Explore Q8Z2X8  Go to UniProtKB:  Q8Z2X8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAV	B [auth A]	(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran C5 H10 O5 BVIYGXUQVXBHQS-IUYQGCFVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.582	α = 90
b = 61.754	β = 90
c = 115.753	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHENIX	phasing
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Gopinath, S., Perumal, P., Rahul, R., Arockiasamy, A., SundaraBaalaji, N.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	2011-15260

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-10-30
  Changes: Structure summary