BMRB Entry 25468

Name: Solution NMR Structure of PDFL2.1 from Arabidopsis thaliana
Published: 2016-02-15

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PDB ID: 2mz0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25468
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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:

Solution NMR Structure of PDFL2.1 from Arabidopsis thaliana

Deposition date:

2015-02-05

Original release date:

2016-02-15

Authors:

Omidvar, Reza; Bohlmann, Holger; Xia, Youlin; Veglia, Gianluigi

Citation:

Citation: Omidvar, Reza; Xia, Youlin; Porcelli, Fernando; Bohlmann, Holger; Veglia, Gianluigi. "NMR structure and conformational dynamics of AtPDFL2.1, a defensin-like peptide from Arabidopsis thaliana." Biochim. Biophys. Acta 1864, 1739-1747 (2016).
PubMed: 27592418

Assembly members:

Assembly members:
entity, polymer, 55 residues, 6152.270 Da.

Natural source:

Natural source: Common Name: thale cress Taxonomy ID: 3702 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Arabidopsis thaliana

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pETtrx_1a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: KDIDGRKPLLIGTCIEFPTE KCNKTCIESNFAGGKCVHIG QSLDFVCVCFPKYYI

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	161
15N chemical shifts	55
1H chemical shifts	386

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 55 residues - 6152.270 Da.

1

LYS

ASP

ILE

ASP

GLY

ARG

LYS

PRO

LEU

2

ILE

GLY

THR

CYS

ILE

GLU

PHE

PRO

THR

GLU

3

LYS

CYS

ASN

LYS

THR

CYS

ILE

GLU

SER

ASN

4

PHE

ALA

GLY

LYS

CYS

VAL

HIS

ILE

GLY

5

GLN

SER

LEU

ASP

PHE

VAL

CYS

VAL

CYS

PHE

6

PRO

LYS

TYR

ILE

Samples:

sample_1: entity, [U-13C; U-15N], 1 mM; potassium chloride 40 mM; potassium phosphate 20 mM; sodium azide 1 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.16 M; pH: 6.5; pressure: 1 atm; temperature: 298 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 HNCO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR_NIH v2.37, Charles Schwieters - structure solution

NMRPipe v7.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.113, Goddard - chemical shift assignment, peak picking

TALOS v3.80F1, Cornilescu, Delaglio and Bax - geometry optimization

TOPSPIN v3.1, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 850 MHz
Bruker Avance 700 MHz

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