BMRBj - BMREntryMaster

Found 1 Document (0.502 seconds)

BMRB: 25704

2N5C

Solution NMR structure of the lasso peptide chaxapeptin

Authors

Elsayed, S.S., Trusch, F., Deng, H., Raab, A., Prokes, I., Busarakam, K., Asenjo, J.A., Andrews, B.A., van West, P., Bull, A.T., Goodfellow, M., Yi, Y., Ebel, R., Jaspars, M., Rateb, M.E.

Assembly

lasso peptide chaxapeptin

Entity

1. lasso peptide chaxapeptin (polymer, Thiol state: not present), 15 monomers, 1632.813 Da Detail

GFGSKPLDSF GLNFF

Formula weight

1632.813 Da

Source organism

Streptomyces leeuwenhoekii

Exptl. method

Refine. method

simulated annealing, distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

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

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	100.0 % (182 of 182)	100.0 % (94 of 94)	100.0 % (73 of 73)	100.0 % (15 of 15)
Backbone	100.0 % (88 of 88)	100.0 % (32 of 32)	100.0 % (42 of 42)	100.0 % (14 of 14)
Sidechain	100.0 % (106 of 106)	100.0 % (62 of 62)	100.0 % (43 of 43)	100.0 % (1 of 1)
Aromatic	100.0 % (40 of 40)	100.0 % (20 of 20)	100.0 % (20 of 20)
Methyl	100.0 % (8 of 8)	100.0 % (4 of 4)	100.0 % (4 of 4)

1. chaxapeptin

GFGSKPLDSF GLNFF

Show sample condition

Sample

Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

Protein Blocks Logo

Calculated from 15 models in PDB: 2N5C, Strand ID: A Detail

Release date

2015-09-29

Citation

Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert
Elsayed, S.S., Trusch, F., Deng, H., Raab, A., Prokes, I., Busarakam, K., Asenjo, J.A., Andrews, B.A., van West, P., Bull, A.T., Goodfellow, M., Yi, Y., Ebel, R., Jaspars, M., Rateb, M.E.
J. Org. Chem. (2015), 80, 10252-10260, PubMed 26402731 , DOI 10.1021/acs.joc.5b01878 , Abstract

Related entities 1. lasso peptide chaxapeptin, : 2 entities Detail

Experiments performed 9 experiments Detail

1 1D 1H

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

2 1D 13C

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

3 1D DEPTQ

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

5 2D 1H-1H COSY

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

7 2D HMBC

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

8 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

9 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz University of Warwick

Sample

State isotropic, Solvent system DMSO, Pressure 1013 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	chaxapeptin	natural abundance		4 mM
2	DMSO	natural abundance		0.0 ~ 0.0 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25704_2n5c.nef
Input source #2: Coordindates	2n5c.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)
1:8:ASP:CG	1:1:GLY:N	unknown	unknown	n/a

Non-standard residues

None

Sequence alignments

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

--------10-----
GFGSKPLDSFGLNFF
|||||||||||||||
GFGSKPLDSFGLNFF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	15	0	0	100.0

Content subtype: combined_25704_2n5c.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	chaxapeptin_assignment	Warning	194		100.0 (chain: A, length: 15)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	203 (1)	noe	100.0 (chain: A, length: 15)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	105 (105)	.	100.0 (chain: A, length: 15)

Assigned chemical shifts

Saveframe: chaxapeptin_assignment
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 99
  - ¹³C chemical shifts: 79
  - ¹⁵N chemical shifts: 16
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
- Total number of restraints: 203
- Weight of restraints: 1.0 (203)
- Potential type of restraints: upper-bound-parabolic (203)
- Range of distance target values: 2.28, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
- Total number of restraints: 105
- Total number of restraints per polymer type: 105
- Weight of restraints: 1.0 (105)
- Potential type of restraints: square-well-parabolic (105)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Lasso peptide