BMRB Entry 34767

Name: NMR Structure of Big-defensin 5 from oyster Crassostrea gigas
Published: 2022-12-09

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PDB ID: 8bgk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34767
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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 Big-defensin 5 from oyster Crassostrea gigas

Deposition date:

2022-10-27

Original release date:

2022-12-09

Authors:

Loth, K.; Asokan, A.

Citation:

Citation: Asokan, A.; Delmas, A.; Aucagne, V.; Loth, K.; Meudal, H.. "Total synthesis and 3D structure determination of a highly hydrophobic antimicrobial Crassostrea gigas big defensin, enduring challenges rescue by a solubilizing tag" .

Assembly members:

Assembly members:
entity_1, polymer, 86 residues, 9977.422 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: WAQALLPIWTYTQXTVSAPL FAALVAAYGIYAVTRYGIKK ARTRNDSHQCANNRGWCRKS CFGHEYIDWYYTDVCGSFYC CRPRNX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	256
15N chemical shifts	73
1H chemical shifts	586

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 86 residues - 9977.422 Da.

1

TRP

ALA

GLN

ALA

LEU

PRO

ILE

TRP

THR

2

TYR

THR

GLN

NLE

THR

VAL

SER

ALA

PRO

LEU

3

PHE

ALA

LEU

VAL

ALA

TYR

GLY

ILE

4

TYR

ALA

VAL

THR

ARG

TYR

GLY

ILE

LYS

5

ALA

ARG

THR

ARG

ASN

ASP

SER

HIS

GLN

CYS

6

ALA

ASN

ARG

GLY

TRP

CYS

ARG

LYS

SER

7

CYS

PHE

GLY

HIS

GLU

TYR

ILE

ASP

TRP

TYR

8

TYR

THR

ASP

VAL

CYS

GLY

SER

PHE

TYR

CYS

9

CYS

ARG

PRO

ARG

ASN

NLW

Samples:

sample_1: Cg-BigDef5 1 mM

sample_conditions_1: ionic strength: 0 mM; pH: 4.7; 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:

TopSpin, Bruker Biospin - collection, processing

CcpNmr Analysis, CCPN - peak picking

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

NMR spectrometers:

Bruker AVANCE III HD 700 700 MHz

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