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BMRB: 17583

2LBZ

Thurincin H

Authors

Sit, C.S., van Belkum, M.J., McKay, R.T., Worobo, R.W., Vederas, J.C.

Assembly

thurincin H

Entity

1. thurincin H (polymer), 31 monomers, 3147.577 Da Detail

DWTCWSCLVC AACSVELLXL VXAAXGAXTA S

Formula weight

3147.577 Da

Source organism

Bacillus thuringiensis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.1 %, Completeness: 88.1 %, Completeness (bb): 93.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.1 % (238 of 270)	90.0 % (117 of 130)	87.4 % (97 of 111)	82.8 % (24 of 29)
Backbone	93.8 % (152 of 162)	94.5 % (52 of 55)	95.0 % (76 of 80)	88.9 % (24 of 27)
Sidechain	83.6 % (112 of 134)	86.7 % (65 of 75)	82.5 % (47 of 57)	0.0 % (0 of 2)
Aromatic	8.3 % (2 of 24)	16.7 % (2 of 12)	0.0 % (0 of 10)	0.0 % (0 of 2)
Methyl	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (22 of 22)

1. thurincin H

DWTCWSCLVC AACSVELLXL VXAAXGAXTA S

Show sample condition

Sample

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

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

Protein Blocks Logo

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

Release date

2011-08-16

Citation

The 3D solution structure of thurincin H, a bacteriocin with four sulfur to α-carbon crosslinks
Sit, C.S., van Belkum, M.J., McKay, R.T., Worobo, R.W., Vederas, J.C.
Angew. Chem Int Ed Engl. (2011), 50, 8718-8721, PubMed 21786372 , DOI 10.1002/anie.201102527 , Abstract

Related entities 1. thurincin H, : 1 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-13C HSQC 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

2 2D 1H-13C 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

3 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

4 3D HNHA

Instrument

Varian INOVA - 500 MHz

Sample

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

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

5 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

6 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

7 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

8 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

9 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

10 3D 1H-13C 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

11 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

12 3D 1H-15N 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	entity	[U-100% 13C; U-100% 15N]		1 mM
2	DSS	natural abundance		100 uM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17583_2lbz.nef
Input source #2: Coordindates	2lbz.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)
1:18:LEU:C	1:19:DSG:N	unknown	unknown	n/a
1:19:DSG:C	1:20:LEU:N	unknown	unknown	n/a
1:27:ALA:C	1:28:DSN:N	unknown	unknown	n/a
1:28:DSN:C	1:29:THR:N	unknown	unknown	n/a
1:13:CYS:SG	1:19:DSG:CA	unknown	unknown	n/a
1:4:CYS:SG	1:28:DSN:CA	unknown	unknown	n/a
1:21:VAL:C	1:22:2TL:N	unknown	unknown	n/a
1:22:2TL:C	1:23:ALA:N	unknown	unknown	n/a
1:24:ALA:C	1:25:2TL:N	unknown	unknown	n/a
1:25:2TL:C	1:26:GLY:N	unknown	unknown	n/a
1:10:CYS:SG	1:22:2TL:CA	unknown	unknown	n/a
1:7:CYS:SG	1:25:2TL:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	19	DSG	D-ASPARAGINE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	22	2TL	D-allothreonine	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	25	2TL	D-allothreonine	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	28	DSN	D-SERINE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--------10--------20--------30-
DWTCWSCLVCAACSVELLXLVXAAXGAXTAS
|||||||||||||||||||||||||||||||
DWTCWSCLVCAACSVELLXLVXAAXGAXTAS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	31	0	0	100.0

Content subtype: combined_17583_2lbz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	12		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	270		100.0 (chain: A, length: 31)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	244 (1)	noe	96.8 (chain: A, length: 31)
2	Distance restraints	DYANA/DIANA_distance_constraints_7	Warning	8 (1)	undefined	25.8 (chain: A, length: 31)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_6	OK	16 (16)	.	58.1 (chain: A, length: 31)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 130
  - ¹³C chemical shifts: 111
  - ¹⁵N chemical shifts: 29
- 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: 31, Sequence coverage: 96.8%
- Total number of restraints: 244
- Weight of restraints: 1.0 (244)
- Potential type of restraints: upper-bound-parabolic (244)
- Range of distance target values: 2.79, 5.5 (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
- Saveframe: DYANA/DIANA_distance_constraints_7
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 25.8%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: upper-bound-parabolic (8)
  - Range of distance target values: 1.6, 2.0 (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_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 58.1%
- Total number of restraints: 16
- Total number of restraints per polymer type: 16
- Weight of restraints: 1.0 (16)
- Potential type of restraints: square-well-parabolic (16)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antimicrobial, bacteriocin, crosslinked, helical loops, post-translationally modified, sulfur to -carbon thioether bridges