BMRB Entry 25916

Name: Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics
Published: 2016-12-01

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PDB ID: 2n9r
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25916
MolProbity Validation Chart

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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:

Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics

Deposition date:

2015-12-03

Original release date:

2016-12-01

Authors:

Irazazabal, Luz; Porto, William; Alves, Eliane; Matos, Carolina; Hancock, Robert; Haney, Evan; Ribeiro, Suzana; Liao, Luciano; Ladram, Ali; Franco, Octavio

Citation:

Citation: Alves, Eliane; Matos, Carolina; Liao, Luciano. "Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics" .

Assembly members:

Assembly members:
entity, polymer, 19 residues, 2112.733 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: obtained from a vendor

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: PKILNKILGKILRLAAAFK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	75
15N chemical shifts	18
1H chemical shifts	135

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 19 residues - 2112.733 Da.

1

PRO

LYS

ILE

LEU

ASN

LYS

ILE

LEU

GLY

LYS

2

ILE

LEU

ARG

LEU

ALA

PHE

LYS

Samples:

sample_1: TSP 5%; D2O 10%; H2O 90%; SDS 100 mM; sodium phosphate 30 mM

sample_conditions_1: pH: 7; 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_1	isotropic	sample_conditions_1
2D 1H-15N sfHMQC	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR_NIH v2.28, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis, geometry optimization

QUEEN, Nabuurs, Spronk, Krieger, Maassen, Vriend and Vuister - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Bruker Avance 500 MHz

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