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BMRB: 34183

6ENA

Nemertide alpha-1

Authors

Jacobsson, E., Rosengren, K.J., Goransson, U.

Assembly

Nemertide alpha-1

Entity

1. Nemertide alpha-1 (polymer), 31 monomers, 3315.780 Da Detail

GCIATGSFCT LSKGCCTKNC GWNFKCNXXN Q

Formula weight

3315.78 Da

Source organism

Lineus longissimus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 79.4 %, Completeness (bb): 81.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.4 % (250 of 315)	93.3 % (152 of 163)	55.6 % (65 of 117)	94.3 % (33 of 35)
Backbone	81.6 % (142 of 174)	98.4 % (61 of 62)	63.9 % (53 of 83)	96.6 % (28 of 29)
Sidechain	79.5 % (132 of 166)	90.1 % (91 of 101)	61.0 % (36 of 59)	83.3 % (5 of 6)
Aromatic	43.8 % (14 of 32)	87.5 % (14 of 16)	0.0 % (0 of 15)	0.0 % (0 of 1)
Methyl	93.8 % (15 of 16)	100.0 % (8 of 8)	87.5 % (7 of 8)

1. entity 1

GCIATGSFCT LSKGCCTKNC GWNFKCNXXN Q

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.1), Details 3 mg/mL Nemertide alpha-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.1), Details 3 mg/mL Nemertide alpha-1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 6ENA, Strand ID: A Detail

Release date

2018-03-04

Citation

Lineus longissimus, the longest animal on earth, expresses peptide toxins targeting voltage gated sodium channels
Jacobsson, E., Andersson, H.S., Strand, M., Peigneur, S., Eriksson, C., Loden, H., Shariatgorji, M., Andren, P.E., Lebbe, K.M., Rosengren, K.J., Tytgat, J., Goransson, U.
Sci. Rep. (2018), DOI:

Related entities 1. Nemertide alpha-1, : 1 : 1 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.1), Details 3 mg/mL Nemertide alpha-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.2), Details 3 mg/mL Nemertide alpha-1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.1), Details 3 mg/mL Nemertide alpha-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.1), Details 3 mg/mL Nemertide alpha-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.2), Details 3 mg/mL Nemertide alpha-1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.2), Details 3 mg/mL Nemertide alpha-1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

7 2D 1H-1H ECOSY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.1 (±0.2), Details 3 mg/mL Nemertide alpha-1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	Nemertide alpha-1	natural abundance		3 (±0.5) mg/mL

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34183_6ena.nef
Input source #2: Coordindates	6ena.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	True (see coodinates for details)
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:2:CYS:SG	A:16:CYS:SG	oxidized, CA 53.964, CB 42.712 ppm	oxidized, CA 53.929, CB 38.301 ppm	2.009
A:9:CYS:SG	A:20:CYS:SG	oxidized, CA 53.008, CB 47.119 ppm	oxidized, CA 54.903, CB 39.502 ppm	2.004
A:15:CYS:SG	A:26:CYS:SG	oxidized, CA 55.426, CB 38.119 ppm	oxidized, CA 54.311, CB 37.191 ppm	2.019

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)
1:27:ASN:C	1:28:HYP:N	unknown	unknown	n/a
1:28:HYP:C	1:29:HYP:N	unknown	unknown	n/a
1:29:HYP:C	1:30:ASN:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	28	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	29	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--------10--------20--------30-
GCIATGSFCTLSKGCCTKNCGWNFKCNXXNQ
|||||||||||||||||||||||||||||||
GCIATGSFCTLSKGCCTKNCGWNFKCNXXNQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	31	0	0	100.0

Content subtype: combined_34183_6ena.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	263		100.0 (chain: A, length: 31)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	459 (1)	noe	100.0 (chain: A, length: 31)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	24 (1)	hbond	54.8 (chain: A, length: 31)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	55 (55)	.	93.5 (chain: A, length: 31)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 160
  - ¹³C chemical shifts: 71
  - ¹⁵N chemical shifts: 32
- 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: CNS/XPLOR_distance_constraints_5
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 100.0%
- Total number of restraints: 459
- Weight of restraints: 1.0 (459)
- Potential type of restraints: square-well-parabolic (459)
- Range of distance target values: 2.1, 3.65 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 54.8%
  - Total number of restraints: 24
  - Weight of restraints: 1.0 (24)
  - Potential type of restraints: square-well-parabolic (24)
  - Range of distance target values: 1.15, 1.65 (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: 31, Sequence coverage: 93.5%
- Total number of restraints: 55
- Total number of restraints per polymer type: 55
- Weight of restraints: 1.0 (55)
- Potential type of restraints: square-well-parabolic (55)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Lineus Longissimus, Nemertea, inhibitor cystine knot, toxin