8TJG

Structure of Nei2 from Mycobacterium smegmatis in complex with Zn2+

• PDB DOI: https://doi.org/10.2210/pdb8TJG/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-21 Released: 2024-03-06 
• Deposition Author(s): Warren, G., Shuman, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.200 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Literature

Structure of Nei2 from Mycobacterium smegmatis in complex with Zn2+

Warren, G., Shuman, S.

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: 28.96 kDa 
• Atom Count: 2,181 
• Modelled Residue Count: 250 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) lyase	A	260	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: nei
UniProt
Find proteins for I7G4T3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7G4T3  Go to UniProtKB:  I7G4T3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.200 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.065	α = 90
b = 57.177	β = 90
c = 66.287	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Warren, G., Shuman, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM126945
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30-GM124165
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release