BMRB Entry 18345

Name: Solution structure of the anti-fungal defensin DEF4 (MTR_8g070770) from Medicago truncatula (barrel clover)
Published: 2012-04-30

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PDB ID: 2lr3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18345
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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 the anti-fungal defensin DEF4 (MTR_8g070770) from Medicago truncatula (barrel clover)

Deposition date:

2012-03-21

Original release date:

2012-04-30

Authors:

Buchko, Garry; Smith, Thomas; Shah, Dilip

Citation:

Citation: Smith, Thomas; Buchko, Garry; Shah, Dilip. "Structure-function analysis of the plant defensin DEF4 from Medicago truncatula (barrel clover)" .

Assembly members:

Assembly members:
entity, polymer, 47 residues, 5355.107 Da.

Natural source:

Natural source: Common Name: barrel medic Taxonomy ID: 3880 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Medicago truncatula

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Pichia pastoris Vector: pPIC9

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: RTCESQSHKFKGPCASDHNC ASVCQTERFSGGRCRGFRRR CFCTTHC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	22
15N chemical shifts	48
1H chemical shifts	254

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	anti-fungal defensin DEF4 (MTR_8g070770)	1

Entities:

Entity 1, anti-fungal defensin DEF4 (MTR_8g070770) 47 residues - 5355.107 Da.

1

ARG

THR

CYS

GLU

SER

GLN

SER

HIS

LYS

PHE

2

LYS

GLY

PRO

CYS

ALA

SER

ASP

HIS

ASN

CYS

3

ALA

SER

VAL

CYS

GLN

THR

GLU

ARG

PHE

SER

4

GLY

ARG

CYS

ARG

GLY

PHE

ARG

5

CYS

PHE

CYS

THR

HIS

CYS

Samples:

sample_1: entity, [U-99% 15N], 1 ± 0.2 mM; TRIS 0.01 ± 0.002 mM; H2O 93%; D2O 7%

sample_2: entity 1 ± 0.2 mM; TRIS 0.01 ± 0.002 mM; H2O 93%; D2O 7%

sample_3: entity, [U-99% 15N], 1 ± 0.2 mM; TRIS 0.01 ± 0.002 mM; D2O 100%

sample_conditions_1: ionic strength: 0.01 M; pH: 4.4; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
deuterium exchange	sample_1	isotropic	sample_conditions_1

Software:

SPARKY v3.115, Goddard - data analysis, peak picking

FELIX v2007, Accelrys Software Inc. - processing

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

PSVS v1.3, Bhattacharya and Montelione - data analysis

NMR spectrometers:

Varian INOVA 600 MHz
Varian VNMRS 750 MHz

PDB	2LR3
GB	AET03453 AFK35827
REF	XP_003628977