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)

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
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Structure of Staphylococcus aureus DinG

Cheng, K., Gao, T., Hao, W.

To be published.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FYH5
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(PTPTPTPT)-3')	A [auth B]	4	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.