BMRB Entry 25974

Name: Structure of calcium-bound form of Penicillium antifungal protein (PAF)
Published: 2017-02-02

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PDB ID: 2nbf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25974
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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:

Structure of calcium-bound form of Penicillium antifungal protein (PAF)

Deposition date:

2016-02-04

Original release date:

2017-02-02

Authors:

Fizil, Adam; Batta, Gyula

Citation:

Citation: Fizil, Adam; Sonderegger, Christoph; Czajlik, Andras; Fekete, Attila; Komaromi, Istvan; Hajdu, Dorottya; Marx, Florentine; Batta, Gyula. "Calcium binding of the antifungal protein PAF: Structure, dynamics and function aspects by NMR and MD simulations." PLoS ONE 13, e0204825-e0204825 (2018).
PubMed: 30321182

Assembly members:

Assembly members:
entity, polymer, 55 residues, 6263.131 Da.
CALCIUM ION, non-polymer, 40.078 Da.

Natural source:

Natural source: Common Name: ascomycetes Taxonomy ID: 5076 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Penicillium chrysogenum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Penicillium chrysogenum Vector: pSK275

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: AKYTGKCTKSKNECKYKNDA GKDTFIKCPKFDNKKCTKDN NKCTVDTYNNAVDCD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	52
1H chemical shifts	298

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 - 6263.131 Da.

1

ALA

LYS

TYR

THR

GLY

LYS

CYS

THR

LYS

SER

2

LYS

ASN

GLU

CYS

LYS

TYR

LYS

ASN

ASP

ALA

3

GLY

LYS

ASP

THR

PHE

ILE

LYS

CYS

PRO

LYS

4

PHE

ASP

ASN

LYS

CYS

THR

LYS

ASP

ASN

5

ASN

LYS

CYS

THR

VAL

ASP

THR

TYR

ASN

6

ALA

VAL

ASP

CYS

ASP

Samples:

sample_1: PAFD19S, [U-100% 15N], 1.0 mM; D2O, [U-2H], 5%; sodium chloride 40 mM; sodium phosphate 10 mM; potassium phosphate 0.04%; Calcium ion 10 mM

sample_conditions_1: ionic strength: 0.02 M; pH: 5.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CYANA v2.1, Guntert, Braun and Wuthrich - structure solution

ATNOS-CANDID, Herrmann, Guntert and Wuthrich - chemical shift assignment, peak picking, structure solution

CCPN_Analysis v2.4, CCPN - chemical shift assignment

NMR spectrometers:

Bruker Avance 500 MHz
Bruker DRX 700 MHz

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