9II8 | pdb_00009ii8

Crystal structure of Staphylococcus aureus DinG protein in complex with ssDNA

• PDB DOI: https://doi.org/10.2210/pdb9II8/pdb
• NAKB: 9II8

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli, Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-19 Released: 2025-06-25 
• Deposition Author(s): Cheng, K.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 
  0.293 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.272 (DCC) 
• R-Value Observed: 
  0.270 (Depositor) 

Starting Model: experimental

Literature

Structure of Staphylococcus aureus DinG

Cheng, K., Gao, T., Hao, W.

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)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 105.65 kDa 
• Atom Count: 7,432 
• Modeled Residue Count: 900 
• Deposited Residue Count: 901 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3'-5' exonuclease DinG	B [auth A]	897	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: dinG, SAOUHSC_01472 EC: 3.1
UniProt
Find proteins for Q2FYH5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FYH5  Go to UniProtKB:  Q2FYH5

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*T)-3')	A [auth B]	4	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free:  0.293 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.272 (DCC) 
• R-Value Observed: 0.270 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.17	α = 90
b = 229.17	β = 90
c = 128.03	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Cheng, K.

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

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release