3E54

Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.231

Literature

Macromolecules
Sequence Display for 3E54

Classification: HYDROLASE / DNA

Total Structure Weight: 52905.86


Macromolecule Entities
Molecule Chains Length Organism Details
RRNA intron-encoded endonuclease A, B 169 Vulcanisaeta distributa EC#: 3.1 IUBMB
Mutation: I65M, I107M
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3') C 13 synthetic I-Vdi141I DNA Target Site
DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3') D 9 synthetic I-Vdi141I DNA Target Site
DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3') E 13 synthetic I-Vdi141I DNA Target Site
DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3') F 9 synthetic I-Vdi141I DNA Target Site

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

D, E, F ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.231
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 66.58 α = 90.00
b = 66.58 β = 90.00
c = 217.91 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-08-13
  • Released Date: 2008-12-30
  • Deposition author(s): Nomura, N., Nomura, Y., Sussman, D., Stoddard, B.L.

Revision History

  • Version 1_0: 2008-12-30

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2014-03-12

    Type: Derived calculations