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BMRB: 16319

2KJF

The solution structure of the circular bacteriocin carnocyclin A (CclA)

Authors

Martin-Visscher, L.A., Gong, X., Duszyk, M., Vederas, J.C.

Assembly

Carnocyclin A

Entity

1. Carnocyclin A (polymer, Thiol state: not present), 60 monomers, 5879.969 Da Detail

LVAYGIAQGT AEKVVSLINA GLTVGSIISI LGGVTVGLSG VFTAVKAAIA KQGIKKAIQL

Formula weight

5879.969 Da

Entity Connection

peptide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	peptide	sing	1:LEU1:N	1:LEU60:C

Source organism

Carnobacterium maltaromaticum

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.3 %, Completeness (bb): 99.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (628 of 652)	94.2 % (308 of 327)	98.1 % (256 of 261)	100.0 % (64 of 64)
Backbone	99.4 % (358 of 360)	98.4 % (127 of 129)	100.0 % (171 of 171)	100.0 % (60 of 60)
Sidechain	93.6 % (321 of 343)	91.4 % (181 of 198)	96.5 % (136 of 141)	100.0 % (4 of 4)
Aromatic	55.6 % (10 of 18)	55.6 % (5 of 9)	55.6 % (5 of 9)
Methyl	100.0 % (114 of 114)	100.0 % (57 of 57)	100.0 % (57 of 57)

1. Carnocyclin A

LVAYGIAQGT AEKVVSLINA GLTVGSIISI LGGVTVGLSG VFTAVKAAIA KQGIKKAIQL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	sodium azide	natural abundance		1 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
8	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
9	sodium phosphate	natural abundance		20 mM
10	EDTA	natural abundance		1 mM
11	sodium azide	natural abundance		1 mM
12	DSS	natural abundance		0.1 mM
13	D2O	natural abundance		100 %

Protein Blocks Logo

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

Release date

2009-09-03

Citation

The three-dimensional structure of carnocyclin A reveals that many circular bacteriocins share a common structural motif
Martin-Visscher, L.A., Gong, X., Duszyk, M., Vederas, J.C.
J. Biol. Chem. (2009), 284, 28674-28681, PubMed 19692336 , DOI 10.1074/jbc.M109.036459 , Abstract

Related entities 1. Carnocyclin A, : 1 : 1 : 8 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	sodium azide	natural abundance		1 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	sodium azide	natural abundance		1 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	sodium azide	natural abundance		1 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	sodium azide	natural abundance		1 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	sodium azide	natural abundance		1 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	sodium azide	natural abundance		1 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
1	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	sodium azide	natural abundance		1 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
8	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
9	sodium phosphate	natural abundance		20 mM
10	EDTA	natural abundance		1 mM
11	sodium azide	natural abundance		1 mM
12	DSS	natural abundance		0.1 mM
13	D2O	natural abundance		100 %

9 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
8	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
9	sodium phosphate	natural abundance		20 mM
10	EDTA	natural abundance		1 mM
11	sodium azide	natural abundance		1 mM
12	DSS	natural abundance		0.1 mM
13	D2O	natural abundance		100 %

10 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
8	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
9	sodium phosphate	natural abundance		20 mM
10	EDTA	natural abundance		1 mM
11	sodium azide	natural abundance		1 mM
12	DSS	natural abundance		0.1 mM
13	D2O	natural abundance		100 %

11 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
8	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
9	sodium phosphate	natural abundance		20 mM
10	EDTA	natural abundance		1 mM
11	sodium azide	natural abundance		1 mM
12	DSS	natural abundance		0.1 mM
13	D2O	natural abundance		100 %

12 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
8	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
9	sodium phosphate	natural abundance		20 mM
10	EDTA	natural abundance		1 mM
11	sodium azide	natural abundance		1 mM
12	DSS	natural abundance		0.1 mM
13	D2O	natural abundance		100 %

13 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.9

#	Name	Isotope labeling	Type	Concentration
8	Carnocyclin A	[U-99% 13C; U-99% 15N]		1 mM
9	sodium phosphate	natural abundance		20 mM
10	EDTA	natural abundance		1 mM
11	sodium azide	natural abundance		1 mM
12	DSS	natural abundance		0.1 mM
13	D2O	natural abundance		100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16319_2kjf.nef
Input source #2: Coordindates	2kjf.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)
1:60:LEU:C	1:1:LEU:N	unknown	unknown	n/a

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60
LVAYGIAQGTAEKVVSLINAGLTVGSIISILGGVTVGLSGVFTAVKAAIAKQGIKKAIQL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LVAYGIAQGTAEKVVSLINAGLTVGSIISILGGVTVGLSGVFTAVKAAIAKQGIKKAIQL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	60	0	0	100.0

Content subtype: combined_16319_2kjf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	629		100.0 (chain: A, length: 60)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	888 (1)	noe	100.0 (chain: A, length: 60)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 60, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 305
  - ¹³C chemical shifts: 260
  - ¹⁵N chemical shifts: 64
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 60, Sequence coverage: 100.0%
- Total number of restraints: 888
- Weight of restraints: 1.0 (888)
- Potential type of restraints: upper-bound-parabolic (888)
- Range of distance target values: 2.89, 5.84 (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

Keywords antimicrobial peptide, circular bacteriocin, helical, saposin-fold, solution NMR