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Found 1 Document (0.457 seconds)

BMRB: 30211

5U9Q

Ocellatin-LB1

Authors

Gusmao, K.A.G., Santos, D.M., de Lima, M.E., Pilo-Veloso, D., Resende, J.M.

Assembly

Ocellatin-K1

Entity

1. Ocellatin-K1 (polymer, Thiol state: not present), 23 monomers, 2191.615 Da Detail

GVVDILKGAA KDIAGHLASK VMX

Formula weight

2191.615 Da

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 84.3 %, Completeness (bb): 81.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.3 % (198 of 235)	91.6 % (109 of 119)	73.4 % (69 of 94)	90.9 % (20 of 22)
Backbone	81.8 % (108 of 132)	97.9 % (46 of 47)	66.7 % (42 of 63)	90.9 % (20 of 22)
Sidechain	89.3 % (109 of 122)	87.5 % (63 of 72)	92.0 % (46 of 50)
Aromatic	25.0 % (1 of 4)	50.0 % (1 of 2)	0.0 % (0 of 2)
Methyl	97.2 % (35 of 36)	100.0 % (18 of 18)	94.4 % (17 of 18)

1. entity 1

GVVDILKGAA KDIAGHLASK VMX

Show sample condition

Sample

Solvent system trifluoroethanol/water, Pressure 1 atm, Temperature 293.15 K, pH 7, Details 2.0 mM Ocellatin-LB1, 20 mM potassium phosphate, 1 mM DSS, 60 % d2 TFE, 40 % H2O, trifluoroethanol/water

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	1 mM
2	H2O	natural abundance	40 %
3	Ocellatin-LB1	natural abundance	2.0 mM
4	TFE	d2	60 %
5	potassium phosphate	natural abundance	20 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 5U9Q, Strand ID: A Detail

Release date

2017-12-04

Citation

NMR structures in different membrane environments of three ocellatin peptides isolated from Leptodactylus labyrinthicus
Gusmao, K., Dos Santos, D.M., Santos, V.M., Cortes, M.E., Reis, P., Santos, V.L., Pilo-Veloso, D., Verly, R.M., de Lima, M.E., Resende, J.M.
Peptides (2018), 103, 72-83, PubMed 29596881 , DOI 10.1016/j.peptides.2018.03.016 , Abstract

Entries sharing articles BMRB: 5 entries Detail

  BMRB: 30212 released on 2017-03-21
    Title Ocellatin-LB2, solution structure in TFE by NMR spectroscopy
  BMRB: 30217 released on 2017-03-21
    Title Ocellatin-LB1, solution structure in SDS micelle by NMR spectroscopy
  BMRB: 30218 released on 2017-03-21
    Title Ocellatin-LB2, solution structure in SDS micelle by NMR spectroscopy
  BMRB: 30219 released on 2017-03-21
    Title Ocellatin-F1, solution structure in SDS micelle by NMR spectroscopy
  BMRB: 30216 released on 2017-02-21
    Title Ocellatin-F1

Related entities 1. Ocellatin-K1, : 1 : 11 : 14 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_30211_5u9q.nef
Input source #2: Coordindates	5u9q.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)
1:22:MET:C	1:23:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	23	NH2	AMINO GROUP	Coordinates

Sequence alignments

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

--------10--------20---
GVVDILKGAAKDIAGHLASKVMX
|||||||||||||||||||||||
GVVDILKGAAKDIAGHLASKVMX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	23	0	0	100.0

Content subtype: combined_30211_5u9q.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	197		95.7 (chain: A, length: 23)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	464 (1)	noe	91.3 (chain: A, length: 23)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	38 (38)	.	95.7 (chain: A, length: 23)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 95.7%
- Total number of assignments
  - ¹H chemical shifts: 109
  - ¹³C chemical shifts: 68
  - ¹⁵N chemical shifts: 20
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	121	109	90.1
¹³C chemical shifts	94	68	72.3
¹⁵N chemical shifts	23	20	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	46	97.9
¹³C chemical shifts	44	22	50.0
¹⁵N chemical shifts	23	20	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	63	85.1
¹³C chemical shifts	50	46	92.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	18	94.7
¹³C chemical shifts	19	17	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	1	50.0
¹³C chemical shifts	2	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 91.3%
- Total number of restraints: 464
- Weight of restraints: 1.0 (464)
- Potential type of restraints: square-well-parabolic (464)
- Range of distance target values: 2.3, 4.2 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 95.7%
- Total number of restraints: 38
- Total number of restraints per polymer type: 38
- Weight of restraints: 1.0 (38)
- Potential type of restraints: square-well-parabolic (38)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords AMPHIPATHIC CHARACTER, ANTIMICROBIAL PEPTIDES, ANTIMICROBIAL PROTEIN, C-TERMINAL CARBOXYAMIDATION, HELIX, OCELLATIN

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Found 1 Document (0.457 seconds)

BMRB: 30211

Sample

Entries sharing articles BMRB: 5 entries Detail

Related entities 1. Ocellatin-K1, : 1 : 11 : 14 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail