BMRB Entry 30749

Name: Solution structure of the seed peptide C2 (VBP-1) from pumpkin
Published: 2020-10-19

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PDB ID: 6wql
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30749
MolProbity Validation Chart

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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 seed peptide C2 (VBP-1) from pumpkin

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, 49 residues, 5844.458 Da.

Natural source:

Natural source: Common Name: Pumpkin Taxonomy ID: 3661 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Cucurbita maxima

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XRGSPRAEYEVCRLRCQVAE RGVEQQRKCEQVCEERLRER EQGRGEDVD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	87
15N chemical shifts	43
1H chemical shifts	311

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 49 residues - 5844.458 Da.

1

PCA

ARG

GLY

SER

PRO

ARG

ALA

GLU

TYR

GLU

2

VAL

CYS

ARG

LEU

ARG

CYS

GLN

VAL

ALA

GLU

3

ARG

GLY

VAL

GLU

GLN

ARG

LYS

CYS

GLU

4

GLN

VAL

CYS

GLU

ARG

LEU

ARG

GLU

ARG

5

GLU

GLN

GLY

ARG

GLY

GLU

ASP

VAL

ASP

Samples:

sample_1: C2 2 mg/mL

sample_conditions_1: ionic strength: 0 mM; pH: 3.5; 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-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

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

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