BMRB Entry 26063

Name: 20 lowest energy ensemble of dermcidin (DCD1L) NMR structure
Published: 2017-07-05

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PDB ID: 2ndk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26063
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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:

20 lowest energy ensemble of dermcidin (DCD1L) NMR structure

Deposition date:

2016-06-29

Original release date:

2017-07-05

Authors:

Tan, Kang Wei; Mok, Yu-Keung

Citation:

Citation: Nguyen, Van Sang; Tan, Kang Wei; Ramesh, Karthik; Chew, Fook Tim; Mok, Yu Keung. "Structural basis for the bacterial membrane insertion of dermcidin peptide, DCD-1L." Sci. Rep. 7, 13923-13923 (2017).
PubMed: 29066724

Assembly members:

Assembly members:
entity, polymer, 48 residues, 4826.549 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: N.A.

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: SSLLEKGLDGAKKAVGGLGK LGKDAVEDLESVGKGAVHDV KDVLDSVL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	45
1H chemical shifts	315

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 48 residues - 4826.549 Da.

1

SER

LEU

GLU

LYS

GLY

LEU

ASP

GLY

2

ALA

LYS

ALA

VAL

GLY

LEU

GLY

LYS

3

LEU

GLY

LYS

ASP

ALA

VAL

GLU

ASP

LEU

GLU

4

SER

VAL

GLY

LYS

GLY

ALA

VAL

HIS

ASP

VAL

5

LYS

ASP

VAL

LEU

ASP

SER

VAL

LEU

Samples:

sample_1: entity, [U-100% 13C; U-100% 15N], 1 mM

sample_conditions_1: ionic strength: 0 M; pH: 7; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

Bruker Avance 800 MHz

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