BMRB Entry 30747

Name: Solution NMR structure of the orbitide xanthoxycyclin D
Published: 2020-08-18

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PDB ID: 6wpv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30747
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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 NMR structure of the orbitide xanthoxycyclin D

Deposition date:

2020-04-28

Original release date:

2020-08-18

Authors:

Rosengren, K.; Payne, C.

Citation:

Citation: Fisher, Mark; Payne, Colton; Chetty, Thaveshini; Crayn, Darren; Berkowitz, Oliver; Whelan, James; Rosengren, K Johan; Mylne, Joshua. "The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides" J. Biol. Chem. 295, 14510-14521 (2020).
PubMed: 32817170

Assembly members:

Assembly members:
entity_1, polymer, 8 residues, 833.971 Da.

Natural source:

Natural source: Common Name: Melicope xanthoxyloides Taxonomy ID: 1312821 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Melicope xanthoxyloides

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GTVAVQFL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	20
1H chemical shifts	45

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 8 residues - 833.971 Da.

1

GLY

THR

VAL

ALA

VAL

GLN

PHE

LEU

Samples:

sample_1: Xanthoxycyclin D 8 ± 0.2 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 DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

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

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

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

TopSpin v4.0.3, Bruker Biospin - processing

NMR spectrometers:

Bruker AVANCE III 700 MHz