BMRBj - BMREntryMaster

Found 1 Document (0.505 seconds)

BMRB: 25363

2MWT

1H and 13C chemical shift assignments and structure calculation for crotalicidin in DPC micelles

Authors

Jimenez, M., Zamora-Carreras, H.

Assembly

crotalicidin in DPC micelles

Entity

1. crotalicidin in DPC micelles (polymer, Thiol state: not present), 34 monomers, 4152.301 Da Detail

KRFKKFFKKV KKSVKKRLKK IFKKPMVIGV TIPF

Formula weight

4152.301 Da

Source organism

Crotalus durissus

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 73.3 %, Completeness (bb): 69.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	73.3 % (344 of 469)	91.6 % (250 of 273)	48.0 % (94 of 196)
Backbone	69.6 % (117 of 168)	98.5 % (66 of 67)	50.5 % (51 of 101)
Sidechain	73.1 % (244 of 334)	89.3 % (184 of 206)	46.9 % (60 of 128)
Aromatic	70.0 % (35 of 50)	92.0 % (23 of 25)	48.0 % (12 of 25)
Methyl	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)

1. crotalicidin

KRFKKFFKKV KKSVKKRLKK IFKKPMVIGV TIPF

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
1	crotalicidin	natural abundance		1 mM
2	DPC	[U-98% 2H]		30 mM
3	DSS	natural abundance		0.1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 76.5 %, Completeness (bb): 72.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	76.5 % (718 of 938)	94.0 % (513 of 546)	52.3 % (205 of 392)
Backbone	72.3 % (243 of 336)	97.8 % (131 of 134)	55.4 % (112 of 202)
Sidechain	77.1 % (515 of 668)	92.7 % (382 of 412)	52.0 % (133 of 256)
Aromatic	70.0 % (70 of 100)	92.0 % (46 of 50)	48.0 % (24 of 50)
Methyl	100.0 % (68 of 68)	100.0 % (34 of 34)	100.0 % (34 of 34)

1. crotalicidin

KRFKKFFKKV KKSVKKRLKK IFKKPMVIGV TIPF

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
1	crotalicidin	natural abundance		1 mM
2	DPC	[U-98% 2H]		30 mM
3	DSS	natural abundance		0.1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

Protein Blocks Logo

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

Release date

2015-11-01

Citation

Structural Dissection of Crotalicidin, a Rattlesnake Venom Cathelicidin, Retrieves a Fragment with Antimicrobial and Antitumor Activity
Borges-Falcao, C., de la Torre, B.G., Perez-Peinado, C., Mayol, X., Zamora-Carreras, H., Jimenez, M., Radis-Baptista, G., Andreu, D.
J. Med. Chem. (2015), 58, 8553-8563, PubMed 26465972 , DOI 10.1021/acs.jmedchem.5b01142 , Abstract

Related entities 1. crotalicidin in DPC micelles, : 1 : 1 : 3 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
1	crotalicidin	natural abundance		1 mM
2	DPC	[U-98% 2H]		30 mM
3	DSS	natural abundance		0.1 mM

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
1	crotalicidin	natural abundance		1 mM
2	DPC	[U-98% 2H]		30 mM
3	DSS	natural abundance		0.1 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
1	crotalicidin	natural abundance		1 mM
2	DPC	[U-98% 2H]		30 mM
3	DSS	natural abundance		0.1 mM

4 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
1	crotalicidin	natural abundance		1 mM
2	DPC	[U-98% 2H]		30 mM
3	DSS	natural abundance		0.1 mM

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
1	crotalicidin	natural abundance		1 mM
2	DPC	[U-98% 2H]		30 mM
3	DSS	natural abundance		0.1 mM

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
1	crotalicidin	natural abundance		1 mM
2	DPC	[U-98% 2H]		30 mM
3	DSS	natural abundance		0.1 mM

7 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

8 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

9 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

10 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

11 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

12 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

13 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

14 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

15 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

16 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	crotalicidin	natural abundance		1 mM
5	DPC	[U-98% 2H]		30 mM
6	DSS	natural abundance		0.1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25363_2mwt.nef
Input source #2: Coordindates	2mwt.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30----
KRFKKFFKKVKKSVKKRLKKIFKKPMVIGVTIPF
||||||||||||||||||||||||||||||||||
KRFKKFFKKVKKSVKKRLKKIFKKPMVIGVTIPF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0

Content subtype: combined_25363_2mwt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	341		100.0 (chain: A, length: 34)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	368		100.0 (chain: A, length: 34)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	682 (1)	noe	100.0 (chain: A, length: 34)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	59 (59)	.	97.1 (chain: A, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 250
  - ¹³C chemical shifts: 91
- 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
Saveframe: assigned_chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 263
  - ¹³C chemical shifts: 105
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of restraints: 682
- Weight of restraints: 1.0 (682)
- Potential type of restraints: upper-bound-parabolic (682)
- Range of distance target values: 2.2, 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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 97.1%
- Total number of restraints: 59
- Total number of restraints per polymer type: 59
- Weight of restraints: 1.0 (59)
- Potential type of restraints: square-well-parabolic (59)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antimicrobial peptide, antitumor peptide, cathelicidin