4OK9

Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans

Thiruselvam, V.Sivaraman, P.Kumarevel, T.Ponnuswamy, M.N.

(2014) Biochem Biophys Res Commun 446: 945-951

  • DOI: https://doi.org/10.1016/j.bbrc.2014.03.036
  • Primary Citation of Related Structures:  
    4OK9, 4OKQ

  • PubMed Abstract: 

    RNA binding proteins control gene expression by the attenuation/antitermination mechanism. HutP is an RNA binding antitermination protein. It regulates the expression of hut operon when it binds with RNA by modulating the secondary structure of single-stranded hut mRNA. HutP necessitates the presence of l-histidine and divalent metal ion to bind with RNA. Herein, we report the crystal structures of ternary complex (HutP-l-histidine-Mg(2+)) and EDTA (0.5 M) treated ternary complex (HutP-l-histidine-Mg(2+)), solved at 1.9 Å and 2.5 Å resolutions, respectively, from Geobacillus thermodenitrificans. The addition of 0.5 M EDTA does not affect the overall metal-ion mediated ternary complex structure and however, the metal ions at the non-specific binding sites are chelated, as evidenced from the results of structural features.


  • Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hut operon positive regulatory protein
A, B
149Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Gene Names: GTNG_0361hutP
UniProt
Find proteins for A4IK89 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IK89 
Go to UniProtKB:  A4IK89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4IK89
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.811α = 90
b = 90.811β = 90
c = 76.672γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata 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: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description