BMRB Entry 34346

Name: NMR Structure of Big-defensin 1 from oyster Crassostrea gigas
Published: 2019-12-06

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PDB ID: 6qbl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34346
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of Big-defensin 1 from oyster Crassostrea gigas

Deposition date:

2018-12-21

Original release date:

2019-12-06

Authors:

Loth, K.; Meudal, H.; Delmas, A.

Citation:

Citation: Loth, K.; Vergnes, A.; Barreto, C.; Voisin, S.; Meudal, H.; Da Silva, J.; Bressan, A.; Belmadi, N.; Bachere, E.; Aucagne, V.; Cazevielle, C.; Marchandin, H.; Rosa, R.; Bulet, P.; Touqui, L.; Delmas, A.; Destoumieux-Garzon, D.. "The Ancestral N-Terminal Domain of Big Defensins Drives Bacterially Triggered Assembly into Antimicrobial Nanonets." Mbio 10, e01821-19-e01821-19 (2019).
PubMed: 31641083

Assembly members:

Assembly members:
entity_1, polymer, 93 residues, 10712.988 Da.

Natural source:

Natural source: Common Name: Pacific oyster Taxonomy ID: 29159 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Crassostrea gigas

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XAQALLPIASYAGLTVSAPV FAALVTVYGAYALYRYNIRR RENSYQRIRSDHDSHSCANN RGWCRPTCFSHEYTDWFNND VCGSYRCCRPGRX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	172
15N chemical shifts	90
1H chemical shifts	628

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 93 residues - 10712.988 Da.

1

PCA

ALA

GLN

ALA

LEU

PRO

ILE

ALA

SER

2

TYR

ALA

GLY

LEU

THR

VAL

SER

ALA

PRO

VAL

3

PHE

ALA

LEU

VAL

THR

VAL

TYR

GLY

ALA

4

TYR

ALA

LEU

TYR

ARG

TYR

ASN

ILE

ARG

5

ARG

GLU

ASN

SER

TYR

GLN

ARG

ILE

ARG

SER

6

ASP

HIS

ASP

SER

HIS

SER

CYS

ALA

ASN

7

ARG

GLY

TRP

CYS

ARG

PRO

THR

CYS

PHE

SER

8

HIS

GLU

TYR

THR

ASP

TRP

PHE

ASN

ASP

9

VAL

CYS

GLY

SER

TYR

ARG

CYS

ARG

PRO

10

GLY

ARG

AAR

Samples:

sample_1: [1-93]Cg-BigDef1 1.0 mM

sample_conditions_1: ionic strength: 0 mM; pH: 4.6; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III HD 700 MHz

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