BMRB Entry 30238

Name: Solution structure of chemically synthesized antilisterial Pediocin PA-1 analog.
Published: 2018-06-21

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PDB ID: 5ukz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30238
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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:

Solution structure of chemically synthesized antilisterial Pediocin PA-1 analog.

Deposition date:

2017-01-23

Original release date:

2018-06-21

Authors:

Bedard, F.; Hammami, R.; Zirah, S.; Rebuffat, S.; Fliss, I.; Biron, E.

Citation:

Citation: Bedard, F.; Hammami, R.; Zirah, S.; Rebuffat, S.; Fliss, I.; Biron, E.. "Synthesis, antimicrobial activity and conformational analysis of the class IIa bacteriocin pediocin PA-1 and analogs thereof" Sci. Rep. 8, 9029-9029 (2018).
PubMed: 29899567

Assembly members:

Assembly members:
entity_1, polymer, 44 residues, 4617.172 Da.

Natural source:

Natural source: Common Name: Pediococcus acidilactici Taxonomy ID: 1254 Superkingdom: Bacteria Kingdom: not available Genus/species: Pediococcus acidilactici

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KYYGNGVTCGKHSCSVDWGK ATTCIINNGALAWATGGHQG NHKC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	222

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 44 residues - 4617.172 Da.

1

LYS

TYR

GLY

ASN

GLY

VAL

THR

CYS

GLY

2

LYS

HIS

SER

CYS

SER

VAL

ASP

TRP

GLY

LYS

3

ALA

THR

CYS

ILE

ASN

GLY

ALA

4

LEU

ALA

TRP

ALA

THR

GLY

HIS

GLN

GLY

5

ASN

HIS

LYS

CYS

Samples:

sample_1: Pediocin PA-1 M31L 3.33 ± .01 mg/mL

sample_conditions_1: pH: 2.8; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D TOCSY	sample_1	anisotropic	sample_conditions_1
2D NOESY	sample_1	anisotropic	sample_conditions_1

Software:

CS-Rosetta v3.7, Shen, Vernon, Baker and Bax - refinement, structure calculation

TOPSPIN v3.5, Bruker Biospin - chemical shift assignment

NMR spectrometers:

Bruker AvanceIII 600 MHz