2OPF

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate

Structural Biology Knowledgebase: 2OPF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.240

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2OPF

Classification: HYDROLASE / DNA

Total Structure Weight: 37554.81


Macromolecule Entities
Molecule Chains Length Organism Details
Endonuclease VIII A 262 Escherichia coli EC#: 3.2.2 IUBMB 4.2.99.18 IUBMB
Mutation: P34T, T112R, R252A
Gene Name(s): nei b0714 JW0704
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3' B 12 synthetic
5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' C 12 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, C 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)
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: 1.85 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.240
  • Space Group: P 43 2 2

Unit Cell:

Length (Å) Angle (°)
a = 73.56 α = 90.00
b = 73.56 β = 90.00
c = 170.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-01-29
  • Released Date: 2008-02-26
  • Deposition author(s): Golan, G., Zharov, D.O., Grollman, A.P., Shoham, G.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4