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BMRB: 36025

5H2S

Solution structure of Tilapia Piscidin 4 (TP4) from Oreochromis niloticus

Authors

Wei, S., Chen, C.

Assembly

Tilapia Piscidin 4

Entity

1. Tilapia Piscidin 4 (polymer, Thiol state: not present), 25 monomers, 2981.558 Da Detail

FIHHIIGGLF SAGKAIHRLI RRRRR

Formula weight

2981.558 Da

Source organism

Oreochromis niloticus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.0 %, Completeness: 93.5 %, Completeness (bb): 94.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	93.5 % (157 of 168)	93.5 % (157 of 168)
Backbone	94.3 % (50 of 53)	94.3 % (50 of 53)
Sidechain	93.0 % (107 of 115)	93.0 % (107 of 115)
Aromatic	62.5 % (10 of 16)	62.5 % (10 of 16)
Methyl	100.0 % (16 of 16)	100.0 % (16 of 16)

1. Piscidin-4

FIHHIIGGLF SAGKAIHRLI RRRRR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5, Details 1.5 mM TP4, 20 mM sodium phosphate, 100 mM U-98% 2H dodecylphosphocholine, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	TP4	natural abundance	protein	1.5 mM
2	dodecylphosphocholine	[U-98% 2H]		100 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5, Details 1.5 mM TP4, 20 mM sodium phosphate, 100 mM U-98% 2H dodecylphosphocholine, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	TP4	natural abundance	protein	1.5 mM
7	dodecylphosphocholine	[U-98% 2H]		100 mM
8	sodium phosphate	natural abundance	buffer	20 mM
9	D2O	[U-2H]	solvent	100 %

Protein Blocks Logo

Calculated from 15 models in PDB: 5H2S, Strand ID: A Detail

Release date

2016-11-08

Citation

Solution structure of Tilapia piscidin 4, an antimicrobial peptide effective against multidrug resistant Helicobacter pylori
Wei, S., Liao, Y., Chen, C.

Related entities 1. Tilapia Piscidin 4, : 1 : 10 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz with a triple (1H, 13C and 15N) resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5, Details 1.5 mM TP4, 20 mM sodium phosphate, 100 mM U-98% 2H dodecylphosphocholine, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	TP4	natural abundance	protein	1.5 mM
2	dodecylphosphocholine	[U-98% 2H]		100 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

2 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz with a triple (1H, 13C and 15N) resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5, Details 1.5 mM TP4, 20 mM sodium phosphate, 100 mM U-98% 2H dodecylphosphocholine, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	TP4	natural abundance	protein	1.5 mM
2	dodecylphosphocholine	[U-98% 2H]		100 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz with a triple (1H, 13C and 15N) resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5, Details 1.5 mM TP4, 20 mM sodium phosphate, 100 mM U-98% 2H dodecylphosphocholine, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	TP4	natural abundance	protein	1.5 mM
2	dodecylphosphocholine	[U-98% 2H]		100 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

4 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz with a triple (1H, 13C and 15N) resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5, Details 1.5 mM TP4, 20 mM sodium phosphate, 100 mM U-98% 2H dodecylphosphocholine, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	TP4	natural abundance	protein	1.5 mM
2	dodecylphosphocholine	[U-98% 2H]		100 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz with a triple (1H, 13C and 15N) resonance cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5, Details 1.5 mM TP4, 20 mM sodium phosphate, 100 mM U-98% 2H dodecylphosphocholine, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	TP4	natural abundance	protein	1.5 mM
7	dodecylphosphocholine	[U-98% 2H]		100 mM
8	sodium phosphate	natural abundance	buffer	20 mM
9	D2O	[U-2H]	solvent	100 %

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz with a triple (1H, 13C and 15N) resonance cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 3.5, Details 1.5 mM TP4, 20 mM sodium phosphate, 100 mM U-98% 2H dodecylphosphocholine, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	TP4	natural abundance	protein	1.5 mM
7	dodecylphosphocholine	[U-98% 2H]		100 mM
8	sodium phosphate	natural abundance	buffer	20 mM
9	D2O	[U-2H]	solvent	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_36025_5h2s.nef
Input source #2: Coordindates	5h2s.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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-----
FIHHIIGGLFSAGKAIHRLIRRRRR
|||||||||||||||||||||||||
FIHHIIGGLFSAGKAIHRLIRRRRR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	25	0	0	100.0

Content subtype: combined_36025_5h2s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	157		96.0 (chain: A, length: 25)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	508 (1)	noe	96.0 (chain: A, length: 25)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	14 (1)	hbond	44.0 (chain: A, length: 25)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	16 (16)	.	80.0 (chain: A, length: 25)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 96.0%
- Total number of assignments
  - ¹H chemical shifts: 157
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 96.0%
- Total number of restraints: 508
- Weight of restraints: 1.0 (508)
- Potential type of restraints: square-well-parabolic (508)
- Range of distance target values: 2.15, 3.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 44.0%
  - Total number of restraints: 14
  - Weight of restraints: 1.0 (14)
  - Potential type of restraints: square-well-parabolic (14)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 80.0%
- Total number of restraints: 16
- Total number of restraints per polymer type: 16
- Weight of restraints: 1.0 (16)
- Potential type of restraints: square-well-parabolic (16)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANTIMICROBIAL PROTEIN, DPC micelle, antimicrobial peptide, piscidin, tilapia piscidin 4