6FBU | pdb_00006fbu

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate

• PDB DOI: https://doi.org/10.2210/pdb6FBU/pdb
• NAKB: 6FBU

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-12-19 Released: 2019-01-30 
• Deposition Author(s): Pomyalov, S., Lansky, S., Golan, G., Zharkov, D.O., Grollman, A.P., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.281 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate

Pomyalov, S., Lansky, S., 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.05 kDa 
• Atom Count: 2,787 
• Modeled Residue Count: 279 
• Deposited Residue Count: 288 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease 8	A	262	Escherichia coli K-12	Mutation(s): 3  Gene Names: nei, b0714, JW0704 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: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3')	B	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')	C	13	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.281 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.34	α = 90
b = 75.34	β = 90
c = 164.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
pointless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Pomyalov, S., Lansky, S., Golan, G., Zharkov, D.O., Grollman, A.P., Shoham, G.

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description