The crystal structure of an extracellular ligand-binding receptor from Rhodopseudomonas palustris HaA2

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

Tan, K.Chang, C.Cuff, M.Osipiuk, J.Landorf, E.Mack, J.C.Zerbs, S.Joachimiak, A.Collart, F.R.

(2013) Proteins 81: 1709-1726

  • DOI: https://doi.org/10.1002/prot.24305
  • Primary Citation of Related Structures:  
    3RPW, 3SG0, 3TX6, 3UK0, 3UKJ, 4DQD, 4EYO, 4EYQ, 4F8J, 4FB4, 4I1D

  • PubMed Abstract: 

    Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins.

  • Organizational Affiliation

    Biosciences Division, Argonne National Laboratory, Lemont, Illinois, 60439; The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, Illinois, 60439; Structural Biology Center, Argonne National Laboratory, Lemont, Illinois, 60439.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular ligand-binding receptor386Rhodopseudomonas palustris HaA2Mutation(s): 0 
Gene Names: Rhodopseudomonas palustrisRPB_4630
Find proteins for Q2IR47 (Rhodopseudomonas palustris (strain HaA2))
Explore Q2IR47 
Go to UniProtKB:  Q2IR47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2IR47
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 173

Download Ideal Coordinates CCD File 
C8 H6 O3
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.494α = 90
b = 70.301β = 90
c = 98.265γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-10-14
    Changes: Database references