BMRB Entry 30561

Name: NMR solution structure of Pisum sativum defensin 2 (Psd2) provides evidence for the presence of hydrophobic surface clusters
Published: 2019-08-16

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PDB ID: 6nom
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30561
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:

NMR solution structure of Pisum sativum defensin 2 (Psd2) provides evidence for the presence of hydrophobic surface clusters

Deposition date:

2019-01-16

Original release date:

2019-08-16

Authors:

Pinheiro-Aguiar, R.; Amaral, V.; Bastos, I.; Kurtenbach, E.; Almeida, F.

Citation:

Citation: Pinheiro-Aguiar, R.; do Amaral, V.; Pereira, I.; Kurtenbach, E.; Almeida, F.. "Nuclear magnetic resonance solution structure of Pisum sativum defensin 2 provides evidence for the presence of hydrophobic surface-clusters." Proteins 88, 242-246 (2019).
PubMed: 31294889

Assembly members:

Assembly members:
entity_1, polymer, 47 residues, 5414.161 Da.

Natural source:

Natural source: Common Name: Garden pea Taxonomy ID: 3888 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Pisum sativum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Komagataella pastoris

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KTCENLSGTFKGPCIPDGNC NKHCRNNEHLLSGRCRDDFR CWCTNRC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	171
15N chemical shifts	44
1H chemical shifts	274

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 47 residues - 5414.161 Da.

1

LYS

THR

CYS

GLU

ASN

LEU

SER

GLY

THR

PHE

2

LYS

GLY

PRO

CYS

ILE

PRO

ASP

GLY

ASN

CYS

3

ASN

LYS

HIS

CYS

ARG

ASN

GLU

HIS

LEU

4

LEU

SER

GLY

ARG

CYS

ARG

ASP

PHE

ARG

5

CYS

TRP

CYS

THR

ASN

ARG

CYS

Samples:

sample_1: Psd2, [U-13C; U-15N], 1 ± 0.005 mM; phosphate buffer 20 mM; NaCl 10 mM

sample_2: Psd2 1 ± 0.005 mM; phosphate buffer 20 mM; NaCl 10 mM

sample_conditions_1: ionic strength: 0.012 M; pH: 5.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	anisotropic	sample_conditions_1
3D HNCACB	sample_1	anisotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	anisotropic	sample_conditions_1
3D HNCA	sample_1	anisotropic	sample_conditions_1
3D HN(CO)CA	sample_1	anisotropic	sample_conditions_1
3D HNCO	sample_1	anisotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	anisotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

TopSpin, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE III 600 MHz

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