4L5J

Crystal structures of the LsrR proteins complexed with phospho-AI-2 and its two different analogs reveal distinct mechanisms for ligand recognition

• PDB DOI: https://doi.org/10.2210/pdb4L5J/pdb

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


• Deposited: 2013-06-11 Released: 2013-11-06 
• Deposition Author(s): Ryu, K.S., Ha, J.H., Eo, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 136.59 kDa 
• Atom Count: 9,508 
• Modelled Residue Count: 1,232 
• Deposited Residue Count: 1,272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator LsrR	A, B, C, D	318	Escherichia coli K-12	Mutation(s): 0  Gene Names: lsrR, ydeW, b1512, JW1505
UniProt
Find proteins for P76141 (Escherichia coli (strain K12)) Explore P76141  Go to UniProtKB:  P76141

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HSX	E [auth A], F [auth B], G [auth C], H [auth D]	5-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-AIHAYLRMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HSX	PDBBind:  4L5J	Kd: 1.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.33	α = 90
b = 80.611	β = 118.01
c = 118.701	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Ryu, K.S., Ha, J.H., Eo, Y.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Structure summary