1VDX | pdb_00001vdx

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

• PDB DOI: https://doi.org/10.2210/pdb1VDX/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-25 Released: 2005-04-12 
• Deposition Author(s): Rehse, P.H., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

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

• PubMed: 16131753 
• DOI: https://doi.org/10.1107/S0907444905017841
• Primary Citation 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.17 kDa 
• Atom Count: 1,530 
• Modeled Residue Count: 184 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein PH0099	A	184	Pyrococcus horikoshii	Mutation(s): 0  EC: 6.5.1.3 (PDB Primary Data), 3.1.4.58 (UniProt)
UniProt
Find proteins for O57823 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57823  Go to UniProtKB:  O57823

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.068	α = 90
b = 45.471	β = 90
c = 93.171	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Rehse, P.H., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description