4OK9 | pdb_00004ok9

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 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 33.06 kDa 
  • Atom Count: 2,457 
  • Modeled Residue Count: 292 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HIS

Query on HIS



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
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

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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