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BMRB: 17492

2L9X

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), 30 monomers, 2770.208 Da Detail

GNAACVIGCI GSCVISEGIG SLVGTAFXLG

Formula weight

2770.208 Da

Source organism

Bacillus thuringiensis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.7 %, Completeness: 93.5 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.5 % (259 of 277)	94.1 % (128 of 136)	91.9 % (102 of 111)	96.7 % (29 of 30)
Backbone	96.0 % (167 of 174)	95.4 % (62 of 65)	96.2 % (77 of 80)	96.6 % (28 of 29)
Sidechain	91.2 % (114 of 125)	93.0 % (66 of 71)	88.7 % (47 of 53)	100.0 % (1 of 1)
Aromatic	0.0 % (0 of 10)	0.0 % (0 of 5)	0.0 % (0 of 5)
Methyl	97.7 % (43 of 44)	100.0 % (22 of 22)	95.5 % (21 of 22)

1. Thuricin

GNAACVIGCI GSCVISEGIG SLVGTAFXLG

Show sample condition

Sample

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

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

Protein Blocks Logo

Calculated from 20 models in PDB: 2L9X, 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

Related entities 1. Thuricin CD, : 1 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

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

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

2 3D HNHA

Instrument

Varian INOVA - 800 MHz

Sample

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

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

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

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

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

4 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

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

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

5 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

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

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

6 rtm-HNCA

Instrument

Varian INOVA - 800 MHz

Sample

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

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

7 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

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

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

8 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

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

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

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Trna	[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_17492_2l9x.nef
Input source #2: Coordindates	2l9x.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)
1:28:DTH:C	1:29:LEU:N	unknown	unknown	n/a
1:5:CYS:SG	1:28:DTH:CA	unknown	unknown	n/a
1:13:CYS:SG	1:21:SER:CA	unknown	unknown	n/a
1:9:CYS:SG	1:25:THR:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	28	DTH	D-THREONINE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--------20--------30
GNAACVIGCIGSCVISEGIGSLVGTAFXLG
||||||||||||||||||||||||||||||
GNAACVIGCIGSCVISEGIGSLVGTAFXLG

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_17492_2l9x.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	266		100.0 (chain: A, length: 30)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	168 (1)	noe	96.7 (chain: A, length: 30)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	38 (38)	.	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: 131
  - ¹³C chemical shifts: 105
  - ¹⁵N chemical shifts: 30
- 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: 96.7%
- Total number of restraints: 168
- Weight of restraints: 1.0 (168)
- Potential type of restraints: upper-bound-parabolic (168)
- Range of distance target values: 2.93, 5.4 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 93.3%
- Total number of restraints: 38
- Total number of restraints per polymer type: 38
- Weight of restraints: 1.0 (38)
- Potential type of restraints: square-well-parabolic (38)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords crosslinked, Cysteine SG to CA thioether bridges, helical loops, post-translationally modified, thuricin CD