4EQ5

DNA ligase from the archaeon Thermococcus sibiricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeon Thermococcus sibiricus.

Petrova, T.E.Bezsudnova, E.Y.Dorokhov, B.D.Slutskaya, E.S.Polyakov, K.M.Dorovatovskiy, P.V.Ravin, N.V.Skryabin, K.G.Kovalchuk, M.V.Popov, V.O.

(2012) Acta Crystallogr.,Sect.F 68: 163-165

  • DOI: 10.1107/S1744309111050913

  • 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 to maintain the integrity of the genome in DNA replic ...

    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 to maintain the integrity of the genome in DNA replication, recombination and repair. A recombinant ATP-dependent DNA ligase from the hyperthermophilic anaerobic archaeon Thermococcus sibiricus was expressed in Escherichia coli and purified. Crystals were grown by vapour diffusion using the hanging-drop method with 17%(w/v) PEG 4000 and 8.5%(v/v) 2-propanol as precipitants. A diffraction experiment was performed with a single crystal, which diffracted X-rays to 3.0 Å resolution. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.590, b = 87.540, c = 126.300 Å.


    Organizational Affiliation

    Bach Institute of Biochemistry, RAS, Moscow, Russian Federation. petrova@impb.psn.ru




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase
A
571Thermococcus sibiricus (strain MM 739 / DSM 12597)Mutation(s): 0 
Gene Names: lig
EC: 6.5.1.6
Find proteins for C6A2U9 (Thermococcus sibiricus (strain MM 739 / DSM 12597))
Go to UniProtKB:  C6A2U9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.590α = 90.00
b = 87.540β = 90.00
c = 126.300γ = 90.00
Software Package:
Software NamePurpose
BALBESphasing
XDSdata scaling
DNAdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release