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BMRB: 25568

2N1N

Solution structure of VSTx1

Authors

Lau, C.HY., King, G.F., Mobli, M.

Assembly

VSTx1

Entity

1. VSTx1 (polymer), 35 monomers, 4090.793 Da Detail

SECGKFMWKC KNSNDCCKDL VCSSRWKWCV LASPF

Formula weight

4090.793 Da

Source organism

Grammostola rosea

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.9 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.9 % (412 of 421)	99.5 % (220 of 221)	95.7 % (154 of 161)	97.4 % (38 of 39)
Backbone	97.6 % (203 of 208)	98.6 % (69 of 70)	97.1 % (101 of 104)	97.1 % (33 of 34)
Sidechain	98.4 % (243 of 247)	100.0 % (151 of 151)	95.6 % (87 of 91)	100.0 % (5 of 5)
Aromatic	92.9 % (52 of 56)	100.0 % (28 of 28)	84.0 % (21 of 25)	100.0 % (3 of 3)
Methyl	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)

1. entity

SECGKFMWKC KNSNDCCKDL VCSSRWKWCV LASPF

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	sodium acetate	natural abundance		20 mM
2	entity	[U-99% 13C; U-99% 15N]		1.7 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N1N, Strand ID: A Detail

Release date

2016-02-28

Citation

Molecular basis of the interaction between gating modifier spider toxins and the voltage sensor of voltage-gated ion channels
Lau, C.H.Y., King, G.F., Mobli, M.
Sci. Rep. (2016), 6, 34333-34333, PubMed 27677715 , DOI 10.1038/srep34333 , Abstract

Related entities 1. VSTx1, : 1 : 2 : 109 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz Equipped with cryogenically cooled probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	sodium acetate	natural abundance		20 mM
2	entity	[U-99% 13C; U-99% 15N]		1.7 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz Equipped with cryogenically cooled probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	sodium acetate	natural abundance		20 mM
2	entity	[U-99% 13C; U-99% 15N]		1.7 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

3 3D HNCACB

Instrument

Bruker Avance - 900 MHz Equipped with cryogenically cooled probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	sodium acetate	natural abundance		20 mM
2	entity	[U-99% 13C; U-99% 15N]		1.7 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

4 3D HNCO

Instrument

Bruker Avance - 900 MHz Equipped with cryogenically cooled probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	sodium acetate	natural abundance		20 mM
2	entity	[U-99% 13C; U-99% 15N]		1.7 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz Equipped with cryogenically cooled probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	sodium acetate	natural abundance		20 mM
2	entity	[U-99% 13C; U-99% 15N]		1.7 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

6 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz Equipped with cryogenically cooled probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	sodium acetate	natural abundance		20 mM
2	entity	[U-99% 13C; U-99% 15N]		1.7 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

7 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz Equipped with cryogenically cooled probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	sodium acetate	natural abundance		20 mM
2	entity	[U-99% 13C; U-99% 15N]		1.7 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25568_2n1n.nef
Input source #2: Coordindates	2n1n.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:3:CYS:SG	A:17:CYS:SG	oxidized, CA 54.337, CB 41.809 ppm	oxidized, CA 54.483, CB 40.134 ppm	1.98
A:10:CYS:SG	A:22:CYS:SG	oxidized, CA 53.609, CB 47.345 ppm	oxidized, CA 54.629, CB 39.843 ppm	1.976
A:16:CYS:SG	A:29:CYS:SG	oxidized, CA 53.682, CB 41.809 ppm	oxidized, CA 56.596, CB 41.518 ppm	1.968

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-----
SECGKFMWKCKNSNDCCKDLVCSSRWKWCVLASPF
|||||||||||||||||||||||||||||||||||
SECGKFMWKCKNSNDCCKDLVCSSRWKWCVLASPF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0

Content subtype: combined_25568_2n1n.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	413		100.0 (chain: A, length: 35)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	18 (1)	undefined	17.1 (chain: A, length: 35)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	28 (1)	hbond	28.6 (chain: A, length: 35)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	54 (54)	.	97.1 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 220
  - ¹³C chemical shifts: 154
  - ¹⁵N chemical shifts: 39
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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_4
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 17.1%
- Total number of restraints: 18
- Weight of restraints: 1.0 (18)
- Potential type of restraints: upper-bound-parabolic (18)
- Range of distance target values: 1.98, 3.5 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 28.6%
  - Total number of restraints: 28
  - Weight of restraints: 1.0 (28)
  - Potential type of restraints: upper-bound-parabolic (28)
  - Range of distance target values: 1.8, 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: DYANA/DIANA_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 97.1%
- Total number of restraints: 54
- Total number of restraints per polymer type: 54
- Weight of restraints: 1.0 (54)
- Potential type of restraints: square-well-parabolic (54)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Peptide