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BMRB: 19683

2MIJ

NMR structure of the S-linked glycopeptide sublancin 168

Authors

Garcia De Gonzalo, C.V., Zhu, L., Oman, T.J., van der Donk, W.A.

Assembly

S-linked glycopeptide sublancin 168

Entity

1. sublancin (polymer), 37 monomers, 3720.270 Da Detail

GLGKAQCAAL WLQCASGGTI GCGGGAVACQ NYRQFCR

2. S-linked glycopeptide sublancin 168, entity GLC (non-polymer), 180.156 Da

Total weight

3900.426 Da

Max. entity weight

3720.27 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS7:SG	1:CYS36:SG
2	disulfide	sing	1:CYS14:SG	1:CYS29:SG

Source organism

Bacillus subtilis

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 75.9 %, Completeness (bb): 82.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.9 % (290 of 382)	93.4 % (183 of 196)	45.5 % (65 of 143)	97.7 % (42 of 43)
Backbone	82.9 % (184 of 222)	100.0 % (82 of 82)	63.1 % (65 of 103)	100.0 % (37 of 37)
Sidechain	70.9 % (134 of 189)	88.6 % (101 of 114)	40.6 % (28 of 69)	83.3 % (5 of 6)
Aromatic	30.0 % (9 of 30)	53.3 % (8 of 15)	0.0 % (0 of 14)	100.0 % (1 of 1)
Methyl	67.6 % (23 of 34)	100.0 % (17 of 17)	35.3 % (6 of 17)

1. sublancin

GLGKAQCAAL WLQCASGGTI GCGGGAVACQ NYRQFCR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	13C,15N-labeled sublancin	[U-98% 13C; U-98% 15N]		2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	sublancin	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	15N-labeled sublancin	[U-100% 15N]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2MIJ, Strand ID: A Detail

Release date

2014-03-09

Citation

NMR structure of the S-linked glycopeptide sublancin 168
Garcia De Gonzalo, C.V., Zhu, L., Oman, T.J., van der Donk, W.A.
ACS Chem. Biol. (2014), 9, 796-801, PubMed 24405370 , DOI 10.1021/cb4008106 , Abstract

Related entities 1. sublancin, : 1 : 1 : 1 entities Detail

Experiments performed 11 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 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	15N-labeled sublancin	[U-100% 15N]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	sublancin	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	sublancin	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	sublancin	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	sublancin	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	13C,15N-labeled sublancin	[U-98% 13C; U-98% 15N]		2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	13C,15N-labeled sublancin	[U-98% 13C; U-98% 15N]		2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	15N-labeled sublancin	[U-100% 15N]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	15N-labeled sublancin	[U-100% 15N]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

10 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	15N-labeled sublancin	[U-100% 15N]		2 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

11 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	13C,15N-labeled sublancin	[U-98% 13C; U-98% 15N]		2 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19683_2mij.nef
Input source #2: Coordindates	2mij.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:7:CYS:SG	A:36:CYS:SG	oxidized, CA 60.891, CB 40.744 ppm	oxidized, CA 55.826, CB 43.065 ppm	2.259
A:14:CYS:SG	A:29:CYS:SG	oxidized, CA 57.758, CB 38.714 ppm	oxidized, CA 56.997, CB 38.88 ppm	2.251

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)
1:22:CYS:SG	2:1:BGC:C1	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	BGC	beta-D-glucopyranose	None

Sequence alignments

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

--------10--------20--------30-------
GLGKAQCAALWLQCASGGTIGCGGGAVACQNYRQFCR
|||||||||||||||||||||||||||||||||||||
GLGKAQCAALWLQCASGGTIGCGGGAVACQNYRQFCR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	37	0	0	100.0

Content subtype: combined_19683_2mij.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	293		100.0 (chain: A, length: 37)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	601 (1)	noe	100.0 (chain: A, length: 37)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 186
  - ¹³C chemical shifts: 65
  - ¹⁵N chemical shifts: 42
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
- Total number of restraints: 601
- Weight of restraints: 1.0 (601)
- Potential type of restraints: square-well-parabolic (601)
- Range of distance target values: 2.15, 7.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords glycopeptide