BMRB Entry 18723

Name: High resolution NMR solution structure of the theta-defensin RTD-1
Published: 2012-11-27

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PDB ID: 2lyf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18723
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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:

High resolution NMR solution structure of the theta-defensin RTD-1

Deposition date:

2012-09-18

Original release date:

2012-11-27

Authors:

Conibear, Anne; Rosengren, K. Johan; Harvey, Peta; Craik, David

Citation:

Citation: Conibear, Anne; Rosengren, K. Johan; Harvey, Peta; Craik, David. "Structural Characterization of the Cyclic Cystine Ladder Motif of -Defensins." Biochemistry 51, 9718-9726 (2012).
PubMed: 23148585

Assembly members:

Assembly members:
RTD-1, polymer, 18 residues, 2110.656 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RTD-1: GFCRCLCRRGVCRCICTR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	41
15N chemical shifts	12
1H chemical shifts	101

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RTD-1	1

Entities:

Entity 1, RTD-1 18 residues - 2110.656 Da.

This is a head-to-tail cyclic peptide with a peptide bond between Arg18 and Gly1.

1

GLY

PHE

CYS

ARG

CYS

LEU

CYS

ARG

GLY

2

VAL

CYS

ARG

CYS

ILE

CYS

THR

ARG

Samples:

sample_1: RTD-1 1.0 mM; H2O 90%; D2O 10%

sample_2: RTD-1 1.0 mM; D2O 100%

sample_conditions_1: pH: 4.0; 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 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H ECOSY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_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
Bruker Avance 900 MHz

GB	AF191100 AF191101
PDB	1HVZ 2LYF