8ZEF | pdb_00008zef

Crystal structure of Staphylococcus aureus DinG protein in complex with ssDNA and Ca2+

• PDB DOI: https://doi.org/10.2210/pdb8ZEF/pdb
• NAKB: 8ZEF

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


• Deposited: 2024-05-06 Released: 2025-05-21 
• Deposition Author(s): Cheng, K., Gao, T., Hao, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 
  0.292 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.283 (Depositor), 0.282 (DCC) 
• R-Value Observed: 
  0.284 (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: 107.81 kDa 
• Atom Count: 7,498 
• Modeled Residue Count: 898 
• Deposited Residue Count: 908 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3'-5' exonuclease DinG	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: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*T)-3')	B	4	chemical production metagenome

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*TP*TP*TP*T)-3')	C	7	chemical production metagenome

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free:  0.292 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.283 (Depositor), 0.282 (DCC) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.855	α = 90
b = 128.045	β = 90
c = 302.999	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Cheng, K., Gao, T., Hao, W.

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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: 2025-05-21
  Type: Initial release