BMRBj - BMREntryMaster

Found 1 Document (0.564 seconds)

BMRB: 19275

2M8V

Solution Structure and Activity Study of Bovicin HJ50, a Particular Type AII Lantibiotic

Authors

Zhang, J., Feng, Y., Wang, J., Zhong, J.

Assembly

Bovicin HJ50

Entity

1. Bovicin HJ50 (polymer, Thiol state: disulfide and other bound), 33 monomers, 3436.056 Da Detail

ADRGWIKXLX KDCPNVISSI CAGTIITACK NCA

Formula weight

3436.056 Da

Entity Connection

covalent 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	covalent	sing	1:DBB8:CB	1:CYS13:SG
2	covalent	sing	1:DBB10:CB	1:CYS32:SG

Source organism

Streptococcus equinus

Exptl. method

solution NMR

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.9 %, Completeness: 89.1 %, Completeness (bb): 79.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	89.1 % (271 of 304)	98.3 % (170 of 173)	77.1 % (101 of 131)
Backbone	79.2 % (122 of 154)	96.8 % (61 of 63)	67.0 % (61 of 91)
Sidechain	99.4 % (178 of 179)	99.1 % (109 of 110)	100.0 % (69 of 69)
Aromatic	100.0 % (11 of 11)	100.0 % (6 of 6)	100.0 % (5 of 5)
Methyl	100.0 % (40 of 40)	100.0 % (20 of 20)	100.0 % (20 of 20)

1. entity 1

ADRGWIKXLX KDCPNVISSI CAGTIITACK NCA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	sodium acetate	[U-2H]	50 mM
3	DSS	natural abundance	0.01 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
4	entity_1	natural abundance	1 mM
5	sodium acetate	[U-2H]	50 mM
6	DSS	natural abundance	0.01 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M8V, Strand ID: A Detail

Release date

2014-05-19

Citation

Type AII lantibiotic bovicin HJ50 with a rare disulfide bond: structure, structure-activity relationships and mode of action
Zhang, J., Feng, Y., Wang, J., Zhong, J.
Biochem. J. (2014), 461, 497-508, PubMed 24814218 , DOI 10.1042/BJ20131524 , Abstract

Related entities 1. Bovicin HJ50, : 1 : 2 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-13C HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	sodium acetate	[U-2H]	50 mM
3	DSS	natural abundance	0.01 %

2 2D DQF-COSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	sodium acetate	[U-2H]	50 mM
3	DSS	natural abundance	0.01 %

3 2D 1H-1H TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	sodium acetate	[U-2H]	50 mM
3	DSS	natural abundance	0.01 %

4 2D 1H-1H NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	sodium acetate	[U-2H]	50 mM
3	DSS	natural abundance	0.01 %

5 2D 1H-13C HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
4	entity_1	natural abundance	1 mM
5	sodium acetate	[U-2H]	50 mM
6	DSS	natural abundance	0.01 %

6 2D 1H-1H TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
4	entity_1	natural abundance	1 mM
5	sodium acetate	[U-2H]	50 mM
6	DSS	natural abundance	0.01 %

7 2D DQF-COSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
4	entity_1	natural abundance	1 mM
5	sodium acetate	[U-2H]	50 mM
6	DSS	natural abundance	0.01 %

8 2D 1H-1H NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
4	entity_1	natural abundance	1 mM
5	sodium acetate	[U-2H]	50 mM
6	DSS	natural abundance	0.01 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19275_2m8v.nef
Input source #2: Coordindates	2m8v.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:21:CYS:SG	A:29:CYS:SG	oxidized, CA 55.23, CB 40.945 ppm	oxidized, CA 56.23, CB 41.976 ppm	2.029

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)
1:7:LYS:C	1:8:DBB:N	unknown	unknown	n/a
1:8:DBB:C	1:9:LEU:N	unknown	unknown	n/a
1:8:DBB:CB	1:13:CYS:SG	unknown	unknown	n/a
1:9:LEU:C	1:10:DBB:N	unknown	unknown	n/a
1:10:DBB:C	1:11:LYS:N	unknown	unknown	n/a
1:10:DBB:CB	1:32:CYS:SG	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	8	DBB	D-ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Coordinates
A	10	DBB	D-ALPHA-AMINOBUTYRIC ACID	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20--------30---
ADRGWIKXLXKDCPNVISSICAGTIITACKNCA
|||||||||||||||||||||||||||||||||
ADRGWIKXLXKDCPNVISSICAGTIITACKNCA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	33	0	0	100.0

Content subtype: combined_19275_2m8v.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	7		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	285		100.0 (chain: A, length: 33)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	564 (1)	noe	93.9 (chain: A, length: 33)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	9 (9)	.	30.3 (chain: A, length: 33)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 179
  - ¹³C chemical shifts: 106
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID
8	DBB
10	DBB

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	173	171	98.8
¹³C chemical shifts	131	100	76.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	62	98.4
¹³C chemical shifts	62	31	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	110	109	99.1
¹³C chemical shifts	69	69	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	20	20	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	5	5	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 93.9%
- Total number of restraints: 564
- Weight of restraints: 1.0 (564)
- Potential type of restraints: square-well-parabolic (564)
- Range of distance target values: 2.19, 3.65 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 30.3%
- Total number of restraints: 9
- Total number of restraints per polymer type: 9
- Weight of restraints: 1.0 (9)
- Potential type of restraints: square-well-parabolic (9)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords lantibiotic

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Found 1 Document (0.564 seconds)

BMRB: 19275

Sample #1

Sample #2

Related entities 1. Bovicin HJ50, : 1 : 2 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 4 contents Detail