1Q3C

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The E2A mutant at 2.3 resolution.

Structural Biology Knowledgebase: 1Q3C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304
  • R-Value Work: 0.245

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Q3C

Classification: HYDROLASE

Total Structure Weight: 30147.47

Macromolecule Entities
Molecule Chains Length Organism Details
Endonuclease VIII A 262 Escherichia coli EC#: 3.2.2 IUBMB
Mutation: E2A, P34T, T112R
Gene Name(s): nei b0714 JW0704

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304
  • R-Value Work: 0.245
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 57.78 α = 90.00
b = 81.07 β = 90.00
c = 169.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-07-29
  • Released Date: 2004-08-03
  • Deposition author(s): Golan, G., Zharkov, D.O., Feinberg, H., Fernandes, A.S., Zaika, E.I., Kycia, J.H., Grollman, A.P., Shoham, G.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4