4EQ5

DNA ligase from the archaeon Thermococcus sibiricus

• PDB DOI: https://doi.org/10.2210/pdb4EQ5/pdb

• Classification: LIGASE
• Organism(s): Thermococcus sibiricus MM 739
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-18 Released: 2012-05-09 
• Deposition Author(s): Petrova, T., 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.357 (Depositor), 0.360 (DCC) 
• R-Value Work: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.277 (Depositor) 

Starting Model: experimental

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

• PubMed: 22297989 
• 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.

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Organizational Affiliation: 

Bach Institute of Biochemistry, RAS, Moscow, Russian Federation. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.16 kDa 
• Atom Count: 3,884 
• Modelled Residue Count: 516 
• Deposited Residue Count: 571 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	571	Thermococcus sibiricus MM 739	Mutation(s): 0  Gene Names: lig, Thermostable ATP-dependent DNA ligase gene Tsib_0885, TSIB_0885 EC: 6.5.1.1 (PDB Primary Data), 6.5.1.6 (UniProt)
UniProt
Find proteins for C6A2U9 (Thermococcus sibiricus (strain DSM 12597 / MM 739)) Explore C6A2U9  Go to UniProtKB:  C6A2U9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	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 (Depositor), 0.360 (DCC) 
• R-Value Work:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.59	α = 90
b = 87.54	β = 90
c = 126.3	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
BALBES	phasing
PHENIX	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Petrova, T., 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.

Revision History  

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