3RR5

DNA ligase from the archaeon Thermococcus sp. 1519


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.018 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.233 

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 68: 1440-1447

  • DOI: 10.1107/S1744309112043394

  • 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, ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase
A
570Thermococcus sp. 1519Mutation(s): 0 
Gene Names: lig
EC: 6.5.1.6
Find proteins for C0LJI8 (Thermococcus sp. 1519)
Go to UniProtKB:  C0LJI8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.018 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.950α = 90.00
b = 85.600β = 90.00
c = 105.960γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
BALBESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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