BMRB Entry 30748

Name: Solution structure of vicilin-buried peptide-10 from cucumber
Published: 2020-10-19

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PDB ID: 6wqj
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30748
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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 vicilin-buried peptide-10 from cucumber

Deposition date:

2020-04-29

Original release date:

2020-10-19

Authors:

Payne, C.; Rosengren, K.

Citation:

Citation: Payne, Colton; Vadlamani, Grishma; Fisher, Mark; Zhang, Jingjing; Clark, Richard; Mylne, Joshua; Rosengren, K Johan. "Defining the Familial Fold of the Vicilin-Buried Peptide Family" J. Nat. Prod. 83, 3030-3040 (2020).
PubMed: 32997497

Assembly members:

Assembly members:
entity_1, polymer, 35 residues, 4328.845 Da.

Natural source:

Natural source: Common Name: Cucumber Taxonomy ID: 3659 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Cucumis sativus

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XKETEICRQWCQVMKPQGGE EQRRCQQECEERLRD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	81
1H chemical shifts	225

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 35 residues - 4328.845 Da.

1

PCA

LYS

GLU

THR

GLU

ILE

CYS

ARG

GLN

TRP

2

CYS

GLN

VAL

MET

LYS

PRO

GLN

GLY

GLU

3

GLU

GLN

ARG

CYS

GLN

GLU

CYS

GLU

4

GLU

ARG

LEU

ARG

ASP

Samples:

sample_1: VBP-10 1.5 mg/mL

sample_2: VBP-10 1.5 mg/mL

sample_conditions_1: ionic strength: 0 mM; pH: 3.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0 mM; pH: 3.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D TOCSY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_2

Software:

TopSpin, Bruker Biospin - processing

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

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

NMR spectrometers:

Bruker AVANCE III 700 MHz