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 
  • R-Value Observed: 0.277 

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Ligand Structure Quality Assessment 


This is version 1.1 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 Struct Biol Cryst Commun 68: 163-165

  • DOI: https://doi.org/10.1107/S1744309111050913
  • Primary Citation of Related Structures:  
    4EQ5

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase571Thermococcus sibiricus MM 739Mutation(s): 0 
Gene Names: ligThermostable ATP-dependent DNA ligase gene Tsib_0885TSIB_0885
EC: 6.5.1.1
UniProt
Find proteins for C6A2U9 (Thermococcus sibiricus (strain DSM 12597 / MM 739))
Explore C6A2U9 
Go to UniProtKB:  C6A2U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6A2U9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.277 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.59α = 90
b = 87.54β = 90
c = 126.3γ = 90
Software Package:
Software NamePurpose
DNAdata collection
BALBESphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description