BMRB Entry 30579

Name: NMR solution structure of vicilin-buried peptide-8 (VBP-8)
Published: 2019-04-18

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PDB ID: 6o3q
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30579
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:

NMR solution structure of vicilin-buried peptide-8 (VBP-8)

Deposition date:

2019-02-27

Original release date:

2019-04-18

Authors:

Rosengren, K.; Payne, C.

Citation:

Citation: Zhang, J.; Payne, C.; Pouvreau, B.; Schaefer, H.; Fisher, M.; Taylor, N.; Berkowitz, O.; Whelan, J.; Rosengren, K.; Mylne, J.. "An ancient peptide family buried within vicilin precursors." ACS Chem. Biol. 14, 979-993 (2019).
PubMed: 30973714

Assembly members:

Assembly members:
entity_1, polymer, 49 residues, 6007.551 Da.

Natural source:

Natural source: Common Name: Tomato Taxonomy ID: 4081 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Solanum lycopersicum

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: RGPDKSYKRLQECQRRCQSE QQGQRLQECQQRCQQEYQRE KGQHQGETN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	90
15N chemical shifts	46
1H chemical shifts	316

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 49 residues - 6007.551 Da.

1

ARG

GLY

PRO

ASP

LYS

SER

TYR

LYS

ARG

LEU

2

GLN

GLU

CYS

GLN

ARG

CYS

GLN

SER

GLU

3

GLN

GLY

GLN

ARG

LEU

GLN

GLU

CYS

GLN

4

GLN

ARG

CYS

GLN

GLU

TYR

GLN

ARG

GLU

5

LYS

GLY

GLN

HIS

GLN

GLY

GLU

THR

ASN

Samples:

sample_1: VBP-8 2 mg/mL

sample_conditions_1: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 288 K

sample_conditions_3: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 293 K

sample_conditions_4: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 303 K

sample_conditions_5: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 308 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-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_4
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_5

Software:

TopSpin v4, Bruker Biospin - collection, processing

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

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

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

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