1ORP

Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Adenine Complex

Structural Biology Knowledgebase: 1ORP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.241

Literature

Macromolecules
Sequence Display for 1ORP

Classification: HYDROLASE / DNA

Total Structure Weight: 33193.99


Macromolecule Entities
Molecule Chains Length Organism Details
Endonuclease III A 226 Geobacillus stearothermophilus
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*AP*GP*AP*CP*AP*TP*GP*GP*AP*C)-3' B 11 synthetic
5'-D(*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3' C 11 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SF4
Query on SF4

A IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PED
Query on PED
C NON-POLYMER C5 H13 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.241
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 67.73 α = 90.00
b = 106.52 β = 90.00
c = 41.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-03-14
  • Released Date: 2003-07-15
  • Deposition author(s): Fromme, J.C., Verdine, G.L.

Revision History

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