BMRB Entry 31249

Name: The specificity and structure of DNA crosslinking by a gut bacterial genotoxin
Published: 2025-11-19

Click here to enlarge.

PDB ID: 9oso
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31249
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

The specificity and structure of DNA crosslinking by a gut bacterial genotoxin

Deposition date:

2025-05-25

Original release date:

2025-11-19

Authors:

D'Souza, V.D.; Balskus, E.

Citation:

Citation: D'Souza, V.D.; Balskus, E.. "The specificity and structure of DNA crosslinking by a gut bacterial genotoxin" .

Assembly members:

Assembly members:
entity_1, polymer, 14 residues, 4313.816 Da.
entity_2, non-polymer, 745.871 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CGCGAXTATTCGCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	15
15N chemical shifts	7
1H chemical shifts	157

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1
3	unit_3	2

Entities:

Entity 1, unit_1 14 residues - 4313.816 Da.

1

DC

DG

DC

DG

DA

A1CEB

DT

DA

DT

2

DC

DG

DC

DG

Entity 2, unit_3 - 745.871 Da.

1

A1CEC

Samples:

sample_1: DNA-COLIBACTIN 1.5 ug/uL; TRIS 10 mM; sodium chloride 10 mM

sample_2: DNA-COLIBACTIN, [U-100% 13C; U-100% 15N], 1.5 ug/uL; TRIS 10 mM; sodium chloride 10 mM

sample_3: DNA-COLIBACTIN, [U-100% 13C; U-100% 15N], 1.5 ug/uL; TRIS 10 mM; sodium chloride 10 mM

sample_4: DNA-COLIBACTIN 1.5 ug/uL; TRIS 10 mM; sodium chloride 10 mM

sample_conditions_1: ionic strength: 20 mM; pH: 8.2; pressure: 1 bar; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMRFx, Bruce Johnson - chemical shift assignment

NMR spectrometers:

Bruker AVANCE II 700 MHz