1VDX

Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii.

Rehse, P.H.Tahirov, T.H.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1207-1212

  • DOI: 10.1107/S0907444905017841
  • Primary Citation of Related Structures:  
    1VDX

  • PubMed Abstract: 
  • Cyclic phosphodiesterase and 2'-5' RNA ligase are members of a superfamily of proteins which share structural similarities even though their homology may be very low. A putative 2'-5' RNA ligase from Pyrococcus horikoshii has been crystallized and it ...

    Cyclic phosphodiesterase and 2'-5' RNA ligase are members of a superfamily of proteins which share structural similarities even though their homology may be very low. A putative 2'-5' RNA ligase from Pyrococcus horikoshii has been crystallized and its X-ray crystallographic structure determined to 2.4 A. The protein crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.07, b = 45.47, c = 93.17 A and one protein monomer in the asymmetric unit. The molecular-replacement probe was a 2'-5' RNA ligase from Thermus thermophilus which shares 30% sequence identity. The P. horikoshii RNA ligase has some structural features that have more in common with a cyclic phosphodiesterase from Arabidopsis thaliana with which it has no significant homology, yet an examination of the electrostatic surface potential clearly defines its relationship to the T. thermophilus RNA ligase. However, the size of the active-site cleft is smaller and less positively charged than that of the T. thermophilus homologue, suggesting that the actual substrate may be smaller than that previously postulated for the latter.


    Organizational Affiliation

    RIKEN Harima Institute, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical protein PH0099A184Pyrococcus horikoshiiMutation(s): 0 
EC: 6.5.1.3 (PDB Primary Data), 3.1.4.58 (UniProt)
Find proteins for O57823 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O57823 
Go to UniProtKB:  O57823
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.068α = 90
b = 45.471β = 90
c = 93.171γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance