BMRB Entry 31028

Name: NMR shows why a small chemical change almost abolishes the antimicrobial activity of GccF
Published: 2023-06-27

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PDB ID: 8dfz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31028
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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 shows why a small chemical change almost abolishes the antimicrobial activity of GccF

Deposition date:

2022-06-23

Original release date:

2023-06-27

Authors:

Harjes, E.; Edwards, P.; Norris, G.

Citation:

Citation: Harjes, Elena; Edwards, Patrick; Bisset, Sean; Patchett, Mark; Jameson, Geoffrey; Yang, Sung-Hyun; Navo, Claudio; Harris, Paul; Brimble, Margaret; Norris, Gillian. "NMR Shows Why a Small Chemical Change Almost Abolishes the Antimicrobial Activity of Glycocin F" Biochemistry 62, 2669-2676 (2023).
PubMed: 37531216

Assembly members:

Assembly members:
entity_1, polymer, 43 residues, 4820.406 Da.
entity_NAG, non-polymer, 221.208 Da.

Natural source:

Natural source: Common Name: Lactiplantibacillus plantarum Taxonomy ID: 1590 Superkingdom: Bacteria Kingdom: not available Genus/species: Lactiplantibacillus plantarum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Lactiplantibacillus plantarum

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KPAWCWYTLAMCGAGYDGTC DYMYSHCFGIKHHSSGSSSY HC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	128
15N chemical shifts	43
1H chemical shifts	241

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

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

Entities:

Entity 1, unit_1 43 residues - 4820.406 Da.

1

LYS

PRO

ALA

TRP

CYS

TRP

TYR

THR

LEU

ALA

2

MET

CYS

GLY

ALA

GLY

TYR

ASP

EW6

GLY

THR

3

CYS

ASP

TYR

MET

TYR

SER

HIS

CYS

PHE

GLY

4

ILE

LYS

HIS

SER

GLY

SER

5

TYR

HIS

CYS

Entity 2, unit_2 - C8 H15 N O6 - 221.208 Da.

1

NAG

Samples:

sample_1: GccF modified, natural abundabnce, 1 mM

sample_conditions_1: ionic strength: 0 mM; pH: 0 Not defined; pressure: 1 atm; temperature: 307 K

Experiments:

Name	Sample	Sample state	Sample conditions
TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
HMBC	sample_1	isotropic	sample_conditions_1
3D 1H-13C TOCSY	sample_1	isotropic	sample_conditions_1

Software:

YASARA, Elmer Krieger - refinement, structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

ATNOS, Hermann - peak picking

NMR spectrometers:

Bruker Bruker Avance 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks