2OPF | pdb_00002opf

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

• PDB DOI: https://doi.org/10.2210/pdb2OPF/pdb
• NAKB: 2OPF

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

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

Starting Model: experimental

Literature

Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues

Golan, G., Zharkov, D.O., Grollman, A.P., Shoham, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.55 kDa 
• Atom Count: 2,910 
• Modeled Residue Count: 279 
• Deposited Residue Count: 286 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease VIII	C [auth A]	262	Escherichia coli	Mutation(s): 1  Gene Names: nei EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for P50465 (Escherichia coli (strain K12)) Explore P50465  Go to UniProtKB:  P50465

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3'	A [auth B]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'	B [auth C]	12	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth C], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.556	α = 90
b = 73.556	β = 90
c = 170.113	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Golan, G., Zharov, D.O., Grollman, A.P., Shoham, G.

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary