BMRB Entry 31000

Name: Solution NMR structure of 8-residue Rosetta-designed cyclic peptide D8.21 in 50% d6-DMSO and 50% water with cis/trans switching
Published: 2022-09-08

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PDB ID: 7ubf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31000
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR structure of 8-residue Rosetta-designed cyclic peptide D8.21 in 50% d6-DMSO and 50% water with cis/trans switching PubMed: 36041435

Deposition date: 2022-03-14 Original release date: 2022-09-08

Authors: Ramelot, T.; Tejero, R.; Montelione, G.

Citation: Bhardwaj, G.; O'Connor, J.; Rettie, S.; Huang, Y.; Ramelot, T.; Mulligan, V.; Alpkilic, G.; Palmer, J.; Bera, A.; Bick, M.; Di Piazza, M.; Li, X.; Hosseinzadeh, P.; Craven, T.; Tejero, R.; Lauko, A.; Choi, R.; Glynn, C.; Dong, L.; Griffin, R.; van Voorhis, W.; Rodriguez, J.; Stewart, L.; Montelione, G.; Craik, D.; Baker, D.. "Accurate de novo design of membrane-traversing macrocycles" Cell 185, 3520-3532 (2022).

Assembly members:
entity_1, polymer, 8 residues, 891.190 Da.

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: XXXLXXXL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	40
15N chemical shifts	4
1H chemical shifts	60

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 8 residues - 891.190 Da.

1

DVA

MLE

DPR

LEU

DVA

MLE

DPR

LEU

Samples:

sample_1: peptide 6 ± 2 mg/L; TMS 0.03 ± 0.003 %

sample_2: peptide 6 ± 2 mg/mL; TMS 0.03 ± 0.003 %

sample_conditions_1: pH: 0.0 Not defined; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 1H	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
1D 1H	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H ROESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N SOFAST	sample_1	isotropic	sample_conditions_1
1H-13C HMBC	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.98.13, Guntert , Mumenthaler, and Wuthrich - refinement, structure calculation

NMRFAM-SPARKY v1.37, Lee, Tonelli, Markley - peak picking

NMRPipe v10.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TopSpin v4.0.9, Bruker Biospin - collection

PdbStat v5.21.6, Tejero, Snyder, Mao, Aramini, Montelione - data analysis

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE II 600 MHz

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