9KQH | pdb_00009kqh

Crystal structure of Finegoldia magna DinG in complex with ssDNA and ADPNP

• PDB DOI: https://doi.org/10.2210/pdb9KQH/pdb
• NAKB: 9KQH

• Classification: HYDROLASE/DNA
• Organism(s): Finegoldia magna ATCC 29328, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-11-25 Released: 2025-12-03 
• Deposition Author(s): Cheng, K., Gao, T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: in silico

Literature

The structural and biochemical investigation of EndoDinG

Cheng, K., Gao, T.

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: 91.73 kDa 
• Atom Count: 6,437 
• Modeled Residue Count: 750 
• Deposited Residue Count: 760 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA 5'-3' helicase	A	748	Finegoldia magna ATCC 29328	Mutation(s): 1  Gene Names: FMG_1294 EC: 5.6.2.3
UniProt
Find proteins for B0S2X2 (Finegoldia magna (strain ATCC 29328 / DSM 20472 / WAL 2508)) Explore B0S2X2  Go to UniProtKB:  B0S2X2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')	B	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)	D [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.857	α = 90
b = 123.534	β = 90
c = 84.472	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Cheng, K., Gao, T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100017
National Natural Science Foundation of China (NSFC)	China	32270043

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release