BMRB Entry 34901

Name: NMR structure of xantholysin A in micellar DPC solution
Published: 2025-02-21

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PDB ID: 8s2a
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34901
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of xantholysin A in micellar DPC solution

Deposition date:

2024-02-16

Original release date:

2025-02-21

Authors:

Kovacs, B.; Geudens, N.; Martins, J.

Citation:

Citation: Kovacs, B.; Geudens, N.; Martins, J.. "NMR structure of xantholysin A in micellar DPC solution" To be published ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 15 residues, 1794.179 Da.

Natural source:

Natural source: Common Name: Pseudomonas putida Taxonomy ID: 303 Superkingdom: Bacteria Kingdom: not available Genus/species: Pseudomonas putida

Experimental source:

Experimental source: Production method: purified from the natural source

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XLXXXXQXXXXLLXI

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	57
1H chemical shifts	121

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 15 residues - 1794.179 Da.

1

IG8

LEU

DGL

DGN

DVA

DLE

GLN

DSN

DVA

DLE

2

DGN

LEU

DGN

ILE

Samples:

sample_1: xantholysin A 3.2 ± 0.05 mM; DPC, [U-2H], 162.9 ± 0.05 mM

sample_conditions_1: ionic strength: 26 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

AmberTools, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - data analysis

TopSpin v3.x, Bruker Biospin - collection, processing

CcpNmr Analysis, Vuister et al. - chemical shift assignment, peak picking

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMR spectrometers:

Bruker AVANCE II 700 MHz