3RR5

DNA ligase from the archaeon Thermococcus sp. 1519


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.

Petrova, T.Bezsudnova, E.Y.Boyko, K.M.Mardanov, A.V.Polyakov, K.M.Volkov, V.V.Kozin, M.Ravin, N.V.Shabalin, I.G.Skryabin, K.G.Stekhanova, T.N.Kovalchuk, M.V.Popov, V.O.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1440-1447

  • DOI: 10.1107/S1744309112043394
  • Primary Citation of Related Structures:  
    3RR5

  • PubMed Abstract: 
  • DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA ...

    DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecules. Two types of overall conformations of archaeal DNA ligase that depend on the relative position of the OB-fold domain have previously been revealed: closed and open extended conformations. The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (LigTh1519) in the crystalline state determined at a resolution of 3.02 Å shows a new relative arrangement of the OB-fold domain which is intermediate between the positions of this domain in the closed and the open extended conformations of previously determined archaeal DNA ligases. However, small-angle X-ray scattering (SAXS) measurements indicate that in solution the LigTh1519 molecule adopts either an open extended conformation or both an intermediate and an open extended conformation with the open extended conformation being dominant.


    Organizational Affiliation

    Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation. petrova@impb.psn.ru



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligaseA570Thermococcus sp. 1519Mutation(s): 0 
Gene Names: lig
EC: 6.5.1.1 (PDB Primary Data), 6.5.1.6 (UniProt)
UniProt
Find proteins for C0LJI8 (Thermococcus sp. 1519)
Explore C0LJI8 
Go to UniProtKB:  C0LJI8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.95α = 90
b = 85.6β = 90
c = 105.96γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
BALBESphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-12-05
    Changes: Database references
  • Version 1.2: 2013-04-03
    Changes: Database references