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BMRB: 19657

2MHV

Solution Structure of Penicillium Antifungal Protein PAF

Authors

Fizil, A., Batta, G.

Assembly

Penicillium Antifungal Protein PAF

Entity

1. Penicillium Antifungal Protein PAF (polymer, Thiol state: all disulfide bound), 55 monomers, 6249.991 Da Detail

AKYTGKCTKS KNECKYKNDA GKDTFIKCPK FDNKKCTKDN NKCTVDTYNN AVDCD

Formula weight

6249.991 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

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 87.0 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.0 % (557 of 640)	87.0 % (295 of 339)	84.6 % (203 of 240)	96.7 % (59 of 61)
Backbone	96.0 % (315 of 328)	95.5 % (106 of 111)	95.7 % (156 of 163)	98.1 % (53 of 54)
Sidechain	80.0 % (292 of 365)	82.9 % (189 of 228)	74.6 % (97 of 130)	85.7 % (6 of 7)
Aromatic	40.9 % (18 of 44)	81.8 % (18 of 22)	0.0 % (0 of 22)
Methyl	86.7 % (26 of 30)	86.7 % (13 of 15)	86.7 % (13 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 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.65 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-12-07

Citation

NMR Analysis of Constrained Cold and Heat Unfolding of the Antifungal Disulfide Protein PAF: 15N-CEST Reveals Hidden Conformers
Fizil, A., Gaspari, Z., Barna, T., Marx, F., Batta, G.
J. Am. Chem. Soc.

Related entities 1. Penicillium Antifungal Protein PAF, : 1 : 6 : 2 : 15 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz for the acquisition of 13C-edited and 15N-edited NOESY spectra

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

5 3D HNCO

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

6 3D HNCA

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

8 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

9 3D H(CCO)NH

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

11 3D HNHA

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz for the acquisition of 13C-edited and 15N-edited NOESY spectra

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

13 3D 1H-15N TOCSY

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

14 3D HCCH-COSY

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

15 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz for the acquisition of 13C-edited and 15N-edited NOESY spectra

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

16 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz for the acquisition of spectra for chemical shift assignment

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		10 (±0.1) mM
2	sodium chloride	natural abundance		40 (±0.1) mM
3	entity	[U-99% 13C; U-99% 15N]		1.7 (±0.1) mM
4	sodium azide	natural abundance		0.6 (±0.1) mM
5	H2O	natural abundance		10 %
6	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19657_2mhv.nef
Input source #2: Coordindates	2mhv.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 53.06, CB 45.295 ppm	oxidized, CA 56.006, CB 41.353 ppm	1.97
A:14:CYS:SG	A:43:CYS:SG	oxidized, CA 53.764, CB 42.192 ppm	unknown, CA 53.541 ppm	1.981
A:28:CYS:SG	A:54:CYS:SG	oxidized, CA 55.191, CB 41.237 ppm	oxidized, CA 53.697, CB 44.199 ppm	2.15

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_19657_2mhv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	565		98.2 (chain: A, length: 55)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	887 (1)	noe	98.2 (chain: A, length: 55)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	254 (251)	.	100.0 (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: 303
  - ¹³C chemical shifts: 203
  - ¹⁵N chemical shifts: 59
- 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: 98.2%
- Total number of restraints: 887
- Weight of restraints: 1.0 (887)
- Potential type of restraints: upper-bound-parabolic (887)
- Range of distance target values: 2.4, 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: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 100.0%
- Total number of restraints: 251
- Total number of restraints per polymer type: 251
- Weight of restraints: 1.0 (251)
- Potential type of restraints: square-well-parabolic (251)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antifungal, basic, chrysogenum, disulfide, penicillium, stable