BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19175

Title: [Asp2]RTD-1   PubMed: 24382674

Deposition date: 2013-04-18 Original release date: 2014-02-03

Authors: Conibear, Anne; Bochen, Alexander; Rosengren, K. Johan; Kessler, Horst; Craik, David

Citation: Conibear, Anne; Bochen, Alexander; Rosengren, K. Johan; Stupar, Petar; Wang, Conan; Kessler, Horst; Craik, David. "The Cyclic Cystine Ladder of Theta-Defensins as a Stable, Bifunctional Scaffold: A Proof-of-Concept Study Using the Integrin-Binding RGD Motif"  ChemBioChem 15, 451-459 (2014).

Assembly members:
[Asp2]RTD-1, polymer, 18 residues, 2078.569 Da.

Natural source:   Common Name: Rhesus monkey   Taxonomy ID: 9544   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Macaca mulatta

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
[Asp2]RTD-1: GDCRCLCRRGVCRCICTR

Data sets:
Data typeCount
13C chemical shifts52
1H chemical shifts116

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1[Asp2]RTD-11

Entities:

Entity 1, [Asp2]RTD-1 18 residues - 2078.569 Da.

Head-to-tail (Arg-Gly) cyclic peptide with disulfide bonds between cystine residues 3-16, 5-14, and 7-12.

1   GLYASPCYSARGCYSLEUCYSARGARGGLY
2   VALCYSARGCYSILECYSTHRARG

Samples:

sample_1: [Asp2]RTD-1 0.7 mM; DSS 10 ug; H2O 90%; D2O 10%

sample_2: [Asp2]RTD-1 0.6 mM; DSS 10 ug; D2O 100%

sample_conditions_1: pH: 3; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H ECOSYsample_2isotropicsample_conditions_1

Software:

CcpNMR v2.1, CCPN - chemical shift assignment, data analysis, peak picking

TOPSPIN v2.1, Bruker Biospin - collection, processing

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v2.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz

Related Database Links:

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