4EFE | pdb_00004efe

crystal structure of DNA ligase

• PDB DOI: https://doi.org/10.2210/pdb4EFE/pdb

• Classification: ligase/ligase inhibitor
• Organism(s): Enterococcus faecalis
• Mutation(s): No 


• Deposited: 2012-03-29 Released: 2013-04-03 
• Deposition Author(s): Wei, Y., Wang, T., Charifson, P., Xu, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.210 (Depositor) 

Literature

crystal structure of DNA ligase

Wang, T., Xu, W., Charifson, P., Wei, Y.

To be published.

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: 38.77 kDa 
• Atom Count: 3,029 
• Modeled Residue Count: 313 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	331	Enterococcus faecalis	Mutation(s): 0  EC: 6.5.1.2
UniProt
Find proteins for Q837V6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837V6  Go to UniProtKB:  Q837V6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMN	D [auth A]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O
0OV	E [auth A]	[4-amino-2-{[(1S,2R)-2-methylcyclohexyl]oxy}-5-oxopyrido[2,3-d]pyrimidin-8(5H)-yl]acetonitrile C16 H19 N5 O2 MZUFVSMPTFUMGZ-PWSUYJOCSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.55	α = 90
b = 86.53	β = 101.02
c = 57.03	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Wei, Y., Wang, T., Charifson, P., Xu, W.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-05-01
  Changes: Other
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations