BMRBj - BMREntryMaster

Found 1 Document (0.665 seconds)

BMRB: 6352

1W9N

Isolation and characterization of epilancin 15X, a novel lantibiotic from a clinical strain of Staphylococcus epidermidis

Authors

Ekkelenkamp, M., Hanssen, M.G.M., Hsu, S.D., de Jong, A., Milatovic, D., Verhoef, J., van Nuland, N.A.J.

Assembly

Epilancin 15X

Entity

1. Epilancin 15X (polymer, Thiol state: all other bound), 31 monomers, 3568.409 Da Detail

XAXIVKXXIK AXKKLCRGFX LXCGCHFXGK K

Formula weight

3568.409 Da

Entity Connection

thioether 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	thioether	sing	1:DAL12:na	1:CYS16:SG
2	thioether	sing	1:ABA20:na	1:CYS23:SG
3	thioether	sing	1:ABA22:na	1:CYS25:SG

Source organism

Staphylococcus epidermidis

Exptl. method

NMR

Refine. method

ARIA

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 74.2 %, Completeness: 93.6 %, Completeness (bb): 92.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	93.6 % (248 of 265)	94.8 % (145 of 153)	92.0 % (103 of 112)
Backbone	92.2 % (106 of 115)	91.8 % (45 of 49)	92.4 % (61 of 66)
Sidechain	94.1 % (160 of 170)	96.2 % (100 of 104)	90.9 % (60 of 66)
Aromatic	100.0 % (24 of 24)	100.0 % (12 of 12)	100.0 % (12 of 12)
Methyl	100.0 % (24 of 24)	100.0 % (12 of 12)	100.0 % (12 of 12)

1. Epilancin 15X

XAXIVKXXIK AXKKLCRGFX LXCGCHFXGK K

Show sample condition

Sample

Temperature 283 K

#	Name	Isotope labeling	Type	Concentration
1	Epilancin 15X			0.8 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 1W9N, Strand ID: A Detail

Release date

2004-10-13

Citation 1

Isolation and structural characterization of epilancin 15X, a novel lantibiotic from a clinical strain of Staphylococcus epidermidis
Ekkelenkamp, M.B., Hanssen, M.G.M., Hsu, S.D., de Jong, A., Milatovic, D., Verhoef, J., van Nuland, N.A.J.
FEBS Lett. (2005), 579, 1917-1922, PubMed 15792796 , DOI 10.1016/j.febslet.2005.01.083 , Abstract

Show more 3 citaions

Citation 2

Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles
Hsu, S.T., Breukink, E., de Kruijff, B., Kaptein, R., Bonvin, A.M., van Nuland, N.A.
Biochemistry (2002), 41, 7670-7676, PubMed 12056898 , DOI 10.1021/bi025679t , Abstract

Citation 3

NMR study of mersacidin and lipid II interaction in dodecylphosphocholine micelles. Conformational changes are a key to antimicrobial activity
Hsu, S.T., Breukink, E., Bierbaum, G., Sahl, H.G., de Kruijff, B., Kaptein, R., van Nuland, N.A., Bonvin, A.M.
J. Biol. Chem. (2003), 278, 13110-13117, PubMed 12562773 , DOI 10.1074/jbc.M211144200 , Abstract

Citation 4

The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics
Hsu, S.T., Breukink, E., Tischenko, E., Lutters, M.A., de Kruijff, B., Kaptein, R., Bonvin, A.M., van Nuland, N.A.
Nat. Struct. Mol. Biol. (2004), 11, 963-967, PubMed 15361862 , DOI 10.1038/nsmb830 , Abstract

Hide non-primary 3 citaions

Related entities 1. Epilancin 15X, : 1 : 2 entities Detail

Experiments performed 4 experiments Detail

#	Name	Isotope labeling	Type	Concentration
2	Epilancin 15X			3.1 mM

#	Name	Isotope labeling	Type	Concentration
2	Epilancin 15X			3.1 mM

#	Name	Isotope labeling	Type	Concentration
2	Epilancin 15X			3.1 mM

#	Name	Isotope labeling	Type	Concentration
2	Epilancin 15X			3.1 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6352_3.str
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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	1	HOP	(1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL	Assigned chemical shifts
1	3	DHA	2-AMINO-ACRYLIC ACID	Assigned chemical shifts
1	7	AA4	2-AMINO-5-HYDROXYPENTANOIC ACID	Assigned chemical shifts
1	8	AA4	2-AMINO-5-HYDROXYPENTANOIC ACID	Assigned chemical shifts
1	12	DAL	D-ALANINE	Assigned chemical shifts
1	20	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts
1	22	ABA	ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts
1	28	AA4	2-AMINO-5-HYDROXYPENTANOIC ACID	Assigned chemical shifts

Content subtype: bmr6352_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chemical_shift_Epilancin_15X_283K	Warning	365		100.0 (chain: 1, length: 31)
1	Chemical shift references	chemical_shift_reference	OK	1		No information

Assigned chemical shifts

Saveframe: chemical_shift_Epilancin_15X_283K

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 31, Sequence coverage: 100.0%

--------10--------20--------30-
XAXIVKXXIKAXKKLCRGFXLXCGCHFXGKK
|||||||||||||||||||||||||||||||
XAXIVKXXIKAXKKLCRGFXLXCGCHFXGKK

Total number of assignments
- ¹³C chemical shifts: 140
- ¹H chemical shifts: 225

Completeness of assignments

Entity_assemble_ID: 1

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
1	HOP
7	AA4
8	AA4
28	AA4

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
6	LYS	HZ1	7.59
6	LYS	HZ2	7.59
6	LYS	HZ3	7.59
10	LYS	HZ1	7.57
10	LYS	HZ2	7.57
10	LYS	HZ3	7.57
12	DAL	C	179.654
13	LYS	HZ1	7.577
13	LYS	HZ2	7.577
13	LYS	HZ3	7.577
14	LYS	HZ1	7.581
14	LYS	HZ2	7.581
14	LYS	HZ3	7.581
17	ARG	CZ	158.259
17	ARG	HH21	6.913
17	ARG	HH22	6.913
17	ARG	HH11	6.483
17	ARG	HH12	6.483
19	PHE	CG	137.172
20	ABA	C	176.762
26	HIS	CG	129.924
27	PHE	CG	137.403
30	LYS	HZ1	7.536
30	LYS	HZ2	7.536
30	LYS	HZ3	7.536
31	LYS	HZ1	7.514
31	LYS	HZ2	7.514
31	LYS	HZ3	7.514

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	123	117	95.1
¹H chemical shifts	169	162	95.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	51	50	98.0
¹H chemical shifts	56	56	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	72	67	93.1
¹H chemical shifts	113	106	93.8

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	15	13	86.7
¹H chemical shifts	15	13	86.7

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	12	12	100.0
¹H chemical shifts	12	12	100.0

Redox state of CYS
Tautomeric state of HIS
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: 1

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Found 1 Document (0.665 seconds)

BMRB: 6352

Sample

Related entities 1. Epilancin 15X, : 1 : 2 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Chemical shift validation 3 contents Detail