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BMRB: 25974

2NBF

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

Authors

Fizil, A., Batta, G.

Assembly

calcium-bound form of Penicillium antifungal protein (PAF)

Entity

1. calcium-bound form of Penicillium antifungal protein (PAF), entity (polymer), 55 monomers, 6249.991 Da Detail

AKYTGKCTKS KNECKYKNDA GKDTFIKCPK FDNKKCTKDN NKCTVDTYNN AVDCD

Formula weight

6249.991 Da

Source organism

Penicillium chrysogenum

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 82.0 %, Completeness (bb): 97.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	82.0 % (328 of 400)	81.1 % (275 of 339)	86.9 % (53 of 61)
Backbone	97.0 % (160 of 165)	97.3 % (108 of 111)	96.3 % (52 of 54)
Sidechain	70.6 % (166 of 235)	72.4 % (165 of 228)	14.3 % (1 of 7)
Aromatic	86.4 % (19 of 22)	86.4 % (19 of 22)
Methyl	93.3 % (14 of 15)	93.3 % (14 of 15)

1. entity

AKYTGKCTKS KNECKYKNDA GKDTFIKCPK FDNKKCTKDN NKCTVDTYNN AVDCD

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	PAFD19S	[U-100% 15N]		1.0 mM
2	D2O	[U-2H]		5 %
3	sodium chloride	natural abundance		40 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		0.04 %
6	Calcium ion	natural abundance		10 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2NBF, Strand ID: A Detail

Release date

2016-02-07

Citation

Calcium binding of the antifungal protein PAF: Structure, dynamics and function aspects by NMR and MD simulations
Fizil, A., Sonderegger, C., Czajlik, A., Fekete, A., Komaromi, I., Hajdu, D., Marx, F., Batta, G.
PLoS One (2018), 13, e0204825-e0204825, PubMed 30321182 , DOI 10.1371/journal.pone.0204825 , Abstract

Related entities 1. calcium-bound form of Penicillium antifungal protein (PAF), entity, : 1 : 6 : 2 : 15 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	PAFD19S	[U-100% 15N]		1.0 mM
2	D2O	[U-2H]		5 %
3	sodium chloride	natural abundance		40 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		0.04 %
6	Calcium ion	natural abundance		10 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	PAFD19S	[U-100% 15N]		1.0 mM
2	D2O	[U-2H]		5 %
3	sodium chloride	natural abundance		40 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		0.04 %
6	Calcium ion	natural abundance		10 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	PAFD19S	[U-100% 15N]		1.0 mM
2	D2O	[U-2H]		5 %
3	sodium chloride	natural abundance		40 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		0.04 %
6	Calcium ion	natural abundance		10 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	PAFD19S	[U-100% 15N]		1.0 mM
2	D2O	[U-2H]		5 %
3	sodium chloride	natural abundance		40 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		0.04 %
6	Calcium ion	natural abundance		10 mM

5 3D 1H-15N TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	PAFD19S	[U-100% 15N]		1.0 mM
2	D2O	[U-2H]		5 %
3	sodium chloride	natural abundance		40 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		0.04 %
6	Calcium ion	natural abundance		10 mM

6 2D 1H-15N HSQC

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	PAFD19S	[U-100% 15N]		1.0 mM
2	D2O	[U-2H]		5 %
3	sodium chloride	natural abundance		40 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		0.04 %
6	Calcium ion	natural abundance		10 mM

7 2D 1H-1H NOESY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	PAFD19S	[U-100% 15N]		1.0 mM
2	D2O	[U-2H]		5 %
3	sodium chloride	natural abundance		40 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		0.04 %
6	Calcium ion	natural abundance		10 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25974_2nbf.nef
Input source #2: Coordindates	2nbf.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:7:CYS:SG	A:36:CYS:SG	unknown	unknown	1.978
A:7:CYS:SG	A:43:CYS:SG	unknown	unknown	2.763
A:14:CYS:SG	A:43:CYS:SG	unknown	unknown	1.997
A:28:CYS:SG	A:54:CYS:SG	unknown	unknown	1.912
A:36:CYS:SG	A:54:CYS:SG	unknown	unknown	2.481

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50-----
AKYTGKCTKSKNECKYKNDAGKDTFIKCPKFDNKKCTKDNNKCTVDTYNNAVDCD
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
AKYTGKCTKSKNECKYKNDAGKDTFIKCPKFDNKKCTKDNNKCTVDTYNNAVDCD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	55	0	0	100.0

Content subtype: combined_25974_2nbf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	322		98.2 (chain: A, length: 55)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	828 (1)	noe	98.2 (chain: A, length: 55)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 270
  - ¹⁵N chemical shifts: 52
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 98.2%
- Total number of restraints: 828
- Weight of restraints: 1.0 (828)
- Potential type of restraints: upper-bound-parabolic (828)
- Range of distance target values: 2.57, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords PAF, antifungal, calcium binding