9IRO | pdb_00009iro

Crystal structure of SeUGI and SAUDG

PDB DOI: https://doi.org/10.2210/pdb9IRO/pdb

Classification: DNA BINDING PROTEIN/INHIBITOR
Organism(s): Staphylococcus aureus, Staphylococcus epidermidis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-16 Released: 2025-07-16
Deposition Author(s): Wang, H.C., Ko, T.P.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.192 (Depositor), 0.191 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Establish a Least-Square Circle Feature Extraction method for identifying new DNA mimic proteins

Liao, B.C., Chen, Y.H., Chou, H.H., Hsu, K.C., Ko, T.P., Liu, C.Y., Lin, S.J., Chen, Y.C., Hsieh, S.Y., Wang, H.C.

To be published.

Macromolecule Content

Total Structure Weight: 41.85 kDa
Atom Count: 2,985
Modeled Residue Count: 339
Deposited Residue Count: 358
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A	226	Staphylococcus aureus	Mutation(s): 0 Gene Names: ung, SAR0586 EC: 3.2.2.27
UniProt
Find proteins for Q2G0J7 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G0J7 Go to UniProtKB: Q2G0J7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G0J7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcus epidermidis uracil-DNA glycosylase inhibitor (SeUGI)	B	132	Staphylococcus epidermidis	Mutation(s): 0
UniProt
Find proteins for A0A141HMG4 (Staphylococcus aureus subsp. aureus RN4220) Explore A0A141HMG4 Go to UniProtKB: A0A141HMG4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A141HMG4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.192 (Depositor), 0.191 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.895	α = 90
b = 75.86	β = 90
c = 77.056	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
MOLREP	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-2000	data processing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	NSTC 112-2628-B-038 -011

Revision History (Full details and data files)

Version 1.0: 2025-07-16
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.