BMRBj - BMREntryMaster

Found 1 Document (0.507 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.507 seconds)

BMRB: 19275

Sample #1

Sample #2

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

Experiments performed 8 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail