3GDE

The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus

Structural Biology Knowledgebase: 3GDE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.215

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3GDE

Classification: LIGASE

Total Structure Weight: 64311.54

Macromolecule Entities
Molecule Chains Length Organism Details
DNA ligase A 558 Archaeoglobus fulgidus EC#: 6.5.1.1 IUBMB
Gene Name(s): lig AF_0623

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.215
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.36 α = 90.00
b = 94.36 β = 90.00
c = 197.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-02-24
  • Released Date: 2009-12-15
  • Deposition author(s): Kim, D.J., Kim, H.-W., Kim, O., Kim, H.S., Lee, S.J., Suh, S.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4