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BMRB: 25957

2NB0

Structure of D19S variant of the Penicillium Antifungal Protein (PAF)

Authors

Fizil, A., Batta, G.

Assembly

D19S variant of the Penicillium Antifungal Protein (PAF)

Entity

1. D19S variant of the Penicillium Antifungal Protein (PAF) (polymer, Thiol state: all disulfide bound), 55 monomers, 6221.981 Da Detail

AKYTGKCTKS KNECKYKNSA GKDTFIKCPK FDNKKCTKDN NKCTVDTYNN AVDCD

Formula weight

6221.981 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS7:SG	1:CYS36:SG
2	disulfide	sing	1:CYS14:SG	1:CYS43:SG
3	disulfide	sing	1:CYS28:SG	1:CYS54:SG

Source organism

Penicillium chrysogenum

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 65.9 %, Completeness (bb): 78.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	65.9 % (422 of 640)	73.7 % (250 of 339)	46.7 % (112 of 240)	98.4 % (60 of 61)
Backbone	78.0 % (256 of 328)	96.4 % (107 of 111)	58.9 % (96 of 163)	98.1 % (53 of 54)
Sidechain	58.9 % (215 of 365)	62.7 % (143 of 228)	50.0 % (65 of 130)	100.0 % (7 of 7)
Aromatic	0.0 % (0 of 44)	0.0 % (0 of 22)	0.0 % (0 of 22)
Methyl	53.3 % (16 of 30)	73.3 % (11 of 15)	33.3 % (5 of 15)

1. PAFD19S

AKYTGKCTKS KNECKYKNSA 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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

LACS Plot; CA

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2NB0, Strand ID: A Detail

Release date

2016-01-27

Citation

D19S Mutation of the Cationic, Cysteine-Rich Protein PAF: Novel Insights into Its Structural Dynamics, Thermal Unfolding and Antifungal Function
Sonderegger, C., Fizil, A., Burtscher, L., Komaromi, I., Czajlik, A., Munoz, A., Hegedus, N., Read, N., Batta, G., Marx, F.
PLoS One (2017), 12, e0169920-e0169920, PubMed 28072824 , DOI 10.1371/journal.pone.0169920 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 26734 released on 2016-01-18
Title D53S/D55S variant of Penicillium Antifungal Protein, PAF

Related entities 1. D19S variant of the Penicillium Antifungal Protein (PAF), : 1 : 1 : 7 : 15 entities Detail

Experiments performed 9 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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

3 2D 1H-1H 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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

4 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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

5 3D HNHA

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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

6 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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

7 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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

8 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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

9 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]		1.7 mM
2	D2O	[U-2H]		5 v/v
3	H2O	natural abundance		95 v/v
4	sodium chloride	natural abundance		40 mM
5	sodium phosphate	natural abundance		10 mM
6	potassium phosphate	natural abundance		0.04 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25957_2nb0.nef
Input source #2: Coordindates	2nb0.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	oxidized, CA 53.048, CB 45.263 ppm	oxidized, CB 41.381 ppm	1.967
A:28:CYS:SG	A:54:CYS:SG	oxidized, CA 56.607, CB 41.134 ppm	oxidized, CA 56.154, CB 44.454 ppm	1.965

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-----
AKYTGKCTKSKNECKYKNSAGKDTFIKCPKFDNKKCTKDNNKCTVDTYNNAVDCD
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
AKYTGKCTKSKNECKYKNSAGKDTFIKCPKFDNKKCTKDNNKCTVDTYNNAVDCD

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_25957_2nb0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	428		96.4 (chain: A, length: 55)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	672 (1)	noe	96.4 (chain: A, length: 55)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	94 (94)	.	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: 96.4%
- Total number of assignments
  - ¹H chemical shifts: 256
  - ¹³C chemical shifts: 112
  - ¹⁵N chemical shifts: 60
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Rotameric state of ILE , LEU, and VAL
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 96.4%
- Total number of restraints: 667
- Weight of restraints: 1.0 (667)
- Potential type of restraints: upper-bound-parabolic (667)
- Range of distance target values: 2.76, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 98.2%
- Total number of restraints: 94
- Total number of restraints per polymer type: 94
- Weight of restraints: 1.0 (94)
- Potential type of restraints: square-well-parabolic (94)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PAF, antifungal, aspartic acid, point mutation, serine