BMRB Entry 30876

Name: Solution NMR structure of an avian defensin, AvBD3, from mallard
Published: 2021-08-09

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PDB ID: 7lzl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30876
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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 NMR structure of an avian defensin, AvBD3, from mallard

Deposition date:

2021-03-10

Original release date:

2021-08-09

Authors:

Rosengren, K.; Andersson, H.

Citation:

Citation: Helin, A.; Chapman, J.; Tolf, C.; Aarts, L.; Bususu, I.; Rosengren, K.; Andersson, H.; Waldenstrom, J.. "Relation between structure and function of three avian beta-defensin 3b variants from mallard (Anas platyrhynchos)" .

Assembly members:

Assembly members:
entity_1, polymer, 37 residues, 4187.849 Da.

Natural source:

Natural source: Common Name: Mallard Taxonomy ID: 8839 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Anas platyrhynchos

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GNSWLCVRRGGNCRFGRCQF AERQIGRCSAFQPCCGR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	94
15N chemical shifts	34
1H chemical shifts	236

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 37 residues - 4187.849 Da.

1

GLY

ASN

SER

TRP

LEU

CYS

VAL

ARG

GLY

2

GLY

ASN

CYS

ARG

PHE

GLY

ARG

CYS

GLN

PHE

3

ALA

GLU

ARG

GLN

ILE

GLY

ARG

CYS

SER

ALA

4

PHE

GLN

PRO

CYS

GLY

ARG

Samples:

sample_1: AvBD3 2 mg/mL

sample_2: AvBD3 2 mg/mL

sample_conditions_1: ionic strength: 0 mM; pH: 4; 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-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1

Software:

TopSpin v3.1, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment

CYANA v3.9, Guntert, Mumenthaler and Wuthrich - structure calculation

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker AVANCE 600 MHz

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