BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18345

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: Smith, Thomas; Buchko, Garry; Shah, Dilip. "Structure-function analysis of the plant defensin DEF4 from Medicago truncatula (barrel clover)"  Not known ., .-..

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

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

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

Entity Sequences (FASTA):
entity: RTCESQSHKFKGPCASDHNC ASVCQTERFSGGRCRGFRRR CFCTTHC

Data sets:
Data typeCount
13C chemical shifts22
15N chemical shifts48
1H chemical shifts254

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

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

Entities:

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

1   ARGTHRCYSGLUSERGLNSERHISLYSPHE
2   LYSGLYPROCYSALASERASPHISASNCYS
3   ALASERVALCYSGLNTHRGLUARGPHESER
4   GLYGLYARGCYSARGGLYPHEARGARGARG
5   CYSPHECYSTHRTHRHISCYS

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
deuterium exchangesample_1isotropicsample_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

Related Database Links:

PDB
GB AET03453 AFK35827
REF XP_003628977

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts