BMRBj - BMREntryMaster

Found 1 Document (0.333 seconds)

BMRB: 30424

6CL3

LyeTxI-b, a synthetic peptide derived from Lycosa erythrognatha spider venom, shows potent antibiotic activity, in vitro and in vivo

Authors

de Lima, M.E., dos Reis, P.V., Resende, J.M., Verly, R.M.

Assembly

Peptide LyeTxI-b

Entity

1. Peptide LyeTxI-b (polymer, Thiol state: not present), 26 monomers, 2720.365 Da Detail

XIWLTALKFL GKNLGKLAKQ QLAKLX

Formula weight

2720.365 Da

Source organism

Lycosa erythrognatha

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.3 %, Completeness: 74.4 %, Completeness (bb): 81.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.4 % (235 of 316)	78.3 % (130 of 166)	63.1 % (77 of 122)	100.0 % (28 of 28)
Backbone	81.9 % (118 of 144)	96.0 % (48 of 50)	65.7 % (46 of 70)	100.0 % (24 of 24)
Sidechain	71.6 % (139 of 194)	70.7 % (82 of 116)	71.6 % (53 of 74)	100.0 % (4 of 4)
Aromatic	54.5 % (12 of 22)	54.5 % (6 of 11)	50.0 % (5 of 10)	100.0 % (1 of 1)
Methyl	70.0 % (28 of 40)	75.0 % (15 of 20)	65.0 % (13 of 20)

1. entity 1

XIWLTALKFL GKNLGKLAKQ QLAKLX

Show sample condition

Sample

Solvent system TFE-d2/H2O (60:40%, v/v), Pressure 1 atm, Temperature 293 K, pH 7.0, Details 2 mM LyeTxI-b, 20 mM phosphate buffer, 1 mM DSS, TFE-d2/H2O (60:40%, v/v)

#	Name	Isotope labeling	Concentration
1	LyeTxI-b	natural abundance	2 mM
2	phosphate buffer	natural abundance	20 mM
3	DSS	natural abundance	1 mM

Release date

2018-05-13

Citation

LyeTxI-b, a Synthetic Peptide Derived From Lycosa erythrognatha Spider Venom, Shows Potent Antibiotic Activity in Vitro and in Vivo
Reis, P., Boff, D., Verly, R.M., Melo-Braga, M.N., Cortes, M.E., Santos, D.M., Pimenta, A., Amaral, F.A., Resende, J.M., de Lima, M.E.
Front. Microbiol. (2018), 9, 667-667, PubMed 29681894 , DOI 10.3389/fmicb.2018.00667 , Abstract

Related entities 1. Peptide LyeTxI-b, : 1 : 3 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30424_6cl3.nef
Input source #2: Coordindates	6cl3.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:25:LEU:C	1:26:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	ACE	ACETYL GROUP	Coordinates
A	25	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates

Sequence alignments

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

0--------10--------20-----
XIWLTALKFLGKNLGKLAKQQLAKLX
||||||||||||||||||||||||||
XIWLTALKFLGKNLGKLAKQQLAKLX
--------10--------20------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	26	0	0	100.0

Content subtype: combined_30424_6cl3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	246		96.2 (chain: A, length: 26)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	326 (1)	noe	92.3 (chain: A, length: 26)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	44 (44)	.	92.3 (chain: A, length: 26)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 96.2%
- Total number of assignments
  - ¹H chemical shifts: 142
  - ¹³C chemical shifts: 75
  - ¹⁵N chemical shifts: 29
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
4	THR	HG1	1.309

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	170	137	80.6
¹³C chemical shifts	124	75	60.5
¹⁵N chemical shifts	29	29	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	50	98.0
¹³C chemical shifts	48	22	45.8
¹⁵N chemical shifts	25	25	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	119	87	73.1
¹³C chemical shifts	76	53	69.7
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	16	76.2
¹³C chemical shifts	21	13	61.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	6	54.5
¹³C chemical shifts	10	5	50.0
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 92.3%
- Total number of restraints: 326
- Weight of restraints: 1.0 (326)
- Potential type of restraints: square-well-parabolic (326)
- Range of distance target values: 2.3, 3.4 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 26, Sequence coverage: 92.3%
- Total number of restraints: 44
- Total number of restraints per polymer type: 44
- Weight of restraints: 1.0 (44)
- Potential type of restraints: square-well-parabolic (44)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANTIMICROBIAL PROTEIN, antimicrobial peptide

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Found 1 Document (0.333 seconds)

BMRB: 30424

Sample

Related entities 1. Peptide LyeTxI-b, : 1 : 3 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail