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BMRB: 17495

2LA0

Trn- peptide of the two-component bacteriocin Thuricin CD

Authors

Sit, C.S., McKay, R.T., Hill, C., Ross, R.P., Vederas, J.C.

Assembly

Thuricin CD

Entity

1. Thuricin CD (polymer, Thiol state: all other bound), 30 monomers, 2868.266 Da Detail

GWVACVGACG TVCLASGGVG TEFAAASXFL

Formula weight

2868.266 Da

Entity Connection

covalent 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	covalent	sing	1:CYS5:SG	1:DTY28:CA
2	covalent	sing	1:CYS9:SG	1:ALA25:CA
3	covalent	sing	1:CYS13:SG	1:THR21:CA

Source organism

Bacillus thuringiensis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.7 %, Completeness: 77.8 %, Completeness (bb): 81.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.8 % (214 of 275)	87.9 % (116 of 132)	61.9 % (70 of 113)	93.3 % (28 of 30)
Backbone	81.0 % (141 of 174)	92.2 % (59 of 64)	66.7 % (54 of 81)	96.6 % (28 of 29)
Sidechain	77.4 % (96 of 124)	83.8 % (57 of 68)	70.9 % (39 of 55)	0.0 % (0 of 1)
Aromatic	15.6 % (5 of 32)	31.3 % (5 of 16)	0.0 % (0 of 15)	0.0 % (0 of 1)
Methyl	100.0 % (40 of 40)	100.0 % (20 of 20)	100.0 % (20 of 20)

1. Thuricin

GWVACVGACG TVCLASGGVG TEFAAASXFL

Show sample condition

Sample

Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

Protein Blocks Logo

Calculated from 20 models in PDB: 2LA0, Strand ID: A Detail

Release date

2011-05-04

Citation

The 3D structure of thuricin CD, a two-component bacteriocin with cysteine sulfur to α-carbon cross-links
Sit, C.S., McKay, R.T., Hill, C., Ross, R., Vederas, J.C.
J. Am. Chem. Soc. (2011), 133, 7680-7683, PubMed 21526839 , DOI 10.1021/ja201802f , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 17492 released on 2011-05-04
Title Trn- peptide of the two-component bacteriocin Thuricin CD

Related entities 1. Thuricin CD, : 1 : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

3 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

4 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

7 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

8 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

11 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system CD3OH, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Trnb	[U-99% 13C; U-99% 15N]		0.5 mM
2	DSS	natural abundance		100 uM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17495_2la0.nef
Input source #2: Coordindates	2la0.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)
1:27:SER:C	1:28:DTY:N	unknown	unknown	n/a
1:28:DTY:C	1:29:PHE:N	unknown	unknown	n/a
1:5:CYS:SG	1:28:DTY:CA	unknown	unknown	n/a
1:9:CYS:SG	1:25:ALA:CA	unknown	unknown	n/a
1:13:CYS:SG	1:21:THR:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	28	DTY	D-TYROSINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20--------30
GWVACVGACGTVCLASGGVGTEFAAASXFL
||||||||||||||||||||||||||||||
GWVACVGACGTVCLASGGVGTEFAAASXFL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	30	0	0	100.0

Content subtype: combined_17495_2la0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	215		100.0 (chain: A, length: 30)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	109 (1)	noe	90.0 (chain: A, length: 30)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_6	OK	33 (33)	.	93.3 (chain: A, length: 30)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 116
  - ¹³C chemical shifts: 70
  - ¹⁵N chemical shifts: 29
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 90.0%
- Total number of restraints: 109
- Weight of restraints: 1.0 (109)
- Potential type of restraints: upper-bound-parabolic (109)
- Range of distance target values: 3.05, 5.02 (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_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 93.3%
- Total number of restraints: 33
- Total number of restraints per polymer type: 33
- Weight of restraints: 1.0 (33)
- Potential type of restraints: square-well-parabolic (33)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords crosslinked, helical loops, post-translationally modified, sulfur to -carbon thioether bridges