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BMRB: 17662

2LDF

Solution structure of the long sarafotoxin srtx-m

Authors

Cordier, F., Zorba, A., Hajj, M., Ducancel, F., Servent, D., Delepierre, M.

Assembly

srtx-m

Entity

1. srtx-m (polymer, Thiol state: all disulfide bound), 24 monomers, 2908.201 Da Detail

CSCNDINDKE CMYFCHQDVI WDEP

Formula weight

2908.201 Da

Source organism

Atractaspis microlepidota

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, coupling_constants

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 99.3 %, Completeness (bb): 97.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	99.3 % (143 of 144)	99.3 % (143 of 144)
Backbone	97.9 % (46 of 47)	97.9 % (46 of 47)
Sidechain	100.0 % (97 of 97)	100.0 % (97 of 97)
Aromatic	100.0 % (17 of 17)	100.0 % (17 of 17)
Methyl	100.0 % (6 of 6)	100.0 % (6 of 6)

1. srtx-m

CSCNDINDKE CMYFCHQDVI WDEP

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2LDF, Strand ID: A Detail

Coupling constant

8 J values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 K, pH 5 Detail

Release date

2012-05-08

Citation

Pharmacological and structural characterization of long-sarafotoxins, a new family of endothelin-like peptides: Role of the C-terminus extension
Mourier, G., Hajj, M., Cordier, F., Zorba, A., Gao, X., Coskun, T., Herbet, A., Marcon, E., Beau, F., Delepierre, M., Ducancel, F., Servent, D.
Biochimie (2012), 94, 461-470, PubMed 21889567 , DOI 10.1016/j.biochi.2011.08.014 , Abstract

Related entities 1. srtx-m, : 1 : 2 : 3 : 73 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz Spectrometer equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz Spectrometer equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz Spectrometer equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz Spectrometer equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz Spectrometer equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 2D 1H-1H TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	srtx-m	natural abundance		1.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17662_2ldf.nef
Input source #2: Coordindates	2ldf.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:1:CYS:SG	A:15:CYS:SG	unknown	unknown	2.036
A:3:CYS:SG	A:11:CYS:SG	unknown	unknown	2.025

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----
CSCNDINDKECMYFCHQDVIWDEP
||||||||||||||||||||||||
CSCNDINDKECMYFCHQDVIWDEP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	24	0	0	100.0

Content subtype: combined_17662_2ldf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	154		100.0 (chain: A, length: 24)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	501 (1)	noe	100.0 (chain: A, length: 24)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	8 (1)	hbond	33.3 (chain: A, length: 24)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 154
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 100.0%
- Total number of restraints: 499
- Weight of restraints: 1.0 (499)
- Potential type of restraints: square-well-parabolic (499)
- Range of distance target values: 1.7, 4.0 (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: 24, Sequence coverage: 33.3%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: square-well-parabolic (8)
  - Range of distance target values: 1.9, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords endothelin-like peptide, long sarafotoxin