BMRB Entry 30827

Name: Solution NMR structure of the dimeric form of the cyclic plant protein PDP-23 in H2O
Published: 2021-01-25

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PDB ID: 7l51
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30827
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR structure of the dimeric form of the cyclic plant protein PDP-23 in H2O PubMed: 34040741

Deposition date: 2020-12-21 Original release date: 2021-01-25

Authors: Payne, C.; Rosengren, K.

Citation: Payne, C.; Franke, B.; Fisher, M.; Hajiaghaalipour, F.; McAleese, C.; Song, A.; Eliasson, C.; Zhang, J.; Jayasena, A.; Vadlamani, G.; Clark, R.; Minchin, R.; Mylne, J.; Rosengren, K.. "A chameleonic macrocyclic peptide with drug delivery applications" Chem. Sci. 12, 6670-6683 (2021).

Assembly members:
entity_1, polymer, 28 residues, 3135.512 Da.

Natural source: Common Name: garden zinnia Taxonomy ID: 34245 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Zinnia elegans

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GFCWHHSCVPSGTCADFPWP LGHQCFPD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	54
15N chemical shifts	23
1H chemical shifts	172

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 28 residues - 3135.512 Da.

1

GLY

PHE

CYS

TRP

HIS

SER

CYS

VAL

PRO

2

SER

GLY

THR

CYS

ALA

ASP

PHE

PRO

TRP

PRO

3

LEU

GLY

HIS

GLN

CYS

PHE

PRO

ASP

Samples:

sample_1: PDP-23 2 mg/mL

sample_conditions_1: ionic strength: 0 mM; pH: 5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0 mM; pH: 5; pressure: 1 atm; temperature: 308 K

sample_conditions_3: ionic strength: 0 mM; pH: 5; pressure: 1 atm; temperature: 303 K

sample_conditions_4: ionic strength: 0 mM; pH: 5; pressure: 1 atm; temperature: 293 K

sample_conditions_5: ionic strength: 0 mM; pH: 5; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D	sample_1	isotropic	sample_conditions_1
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 TOCSY	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_5
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_4
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_3

Software:

TopSpin, Bruker Biospin - collection, processing

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

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

NMR spectrometers:

Bruker AVANCE III HD 700 MHz
Bruker AVANCE III HD 600 MHz

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