9N2N | pdb_00009n2n

Structure of M tuberculosis NapA bound to 20mer AT rich DNA

• PDB DOI: https://doi.org/10.2210/pdb9N2N/pdb
• NAKB: 9N2N

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Mycobacterium tuberculosis, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-29 Released: 2025-10-22 
• Deposition Author(s): Schumacher, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.87 Å
• R-Value Free: 
  0.328 (Depositor), 0.325 (DCC) 
• R-Value Work: 
  0.300 (Depositor), 0.302 (DCC) 
• R-Value Observed: 
  0.307 (Depositor) 

Starting Model: experimental

Literature

Structure of M tuberculosis NapA bound to 20mer AT rich DNA

Schumacher, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 33.02 kDa 
• Atom Count: 1,321 
• Modeled Residue Count: 145 
• Deposited Residue Count: 218 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fis family transcriptional regulator	A [auth U], B [auth A]	89	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  A4S10_00456, DKC2_0461, DSI80_09725, ERS007657_03567, ERS007679_01808, ERS007681_02029, ERS007688_00846, ERS007718_00086, ERS007741_01318, ERS027646_00220, ERS027659_01205, ERS027661_02888, ERS053720_01018
UniProt
Find proteins for P96276 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P96276  Go to UniProtKB:  P96276

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*TP*TP*TP*AP*TP*T)-3')	C [auth E], D [auth F]	20	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.87 Å
• R-Value Free:  0.328 (Depositor), 0.325 (DCC) 
• R-Value Work:  0.300 (Depositor), 0.302 (DCC) 
• R-Value Observed: 0.307 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.031	α = 90
b = 92.031	β = 90
c = 107.392	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Schumacher, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM130290

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release