BMRB: 25192

Haddock model of Bacillus subtilis L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide

Authors

Schanda, P., Triboulet, S., Laguri, C., Bougault, C., Ayala, I., Callon, M., Arthur, M., Simorre, J.

Assembly

L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide

Entity

1. L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide, entity 1 (polymer, Thiol state: all free), 169 monomers, 18110.66 Da Detail

GRKLLTYQVK QGDTLNSIAA DFRISTAALL QANPSLQAGL TAGQSIVIPG LPDPYTIPYH IAVSIGAKTL TLSLNNRVMK TYPIAVGKIL TQTPTGEFYI INRQRNPGGP FGAYWLSLSK QHYGIHGTNN PASIGKAVSK GCIRMHNKDV IELASIVPNG TRVTINRGS

2. L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide, entity 2 (polymer, Thiol state: not present), 12 monomers, 2888.700 Da
3. L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide, entity 3 (polymer, Thiol state: not present), 4 monomers, 461.4662 × 5 Da Detail

AXXX

Total weight

23306.691 Da

Max. entity weight

18110.66 Da

Source organism

Bacillus subtilis

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 57.8 %, Completeness: 25.2 %, Completeness (bb): 38.0 % Detail

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Polymer type: polypeptide(L) polysaccharide(D)

	Total	1H	13C	15N
All	25.2 % (487 of 1929)	21.1 % (211 of 998)	22.8 % (172 of 753)	58.4 % (104 of 178)
Backbone	38.0 % (377 of 992)	37.2 % (128 of 344)	29.6 % (145 of 490)	65.8 % (104 of 158)
Sidechain	12.6 % (137 of 1089)	12.8 % (84 of 654)	12.8 % (53 of 415)	0.0 % (0 of 20)
Aromatic	0.0 % (0 of 114)	0.0 % (0 of 57)	0.0 % (0 of 56)	0.0 % (0 of 1)
Methyl	17.7 % (39 of 220)	18.2 % (20 of 110)	17.3 % (19 of 110)

1. entity 1

GRKLLTYQVK QGDTLNSIAA DFRISTAALL QANPSLQAGL TAGQSIVIPG LPDPYTIPYH IAVSIGAKTL TLSLNNRVMK TYPIAVGKIL TQTPTGEFYI INRQRNPGGP FGAYWLSLSK QHYGIHGTNN PASIGKAVSK GCIRMHNKDV IELASIVPNG TRVTINRGS

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Sample #1

Solvent system 50 mM HEPES, pH 7.2, Pressure 1 atm, Temperature 298 (±0.2) K, pH 7.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		2.5 mg/mL
2	entity_2	natural abundance		3 mg/mL
3	HEPES	natural abundance		50 mM

Sample #2

Solvent system 50 mM HEPES, pH 7.2, Pressure 1 atm, Temperature 298 (±0.2) K, pH 7.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]		376 uM
5	HEPES	natural abundance		50 mM

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Chem. Shift Complete2

Sequence coverage: 58.9 %, Completeness: 23.3 %, Completeness (bb): 36.7 % Detail

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Polymer type: polypeptide(L) polysaccharide(D)

	Total	1H	13C	15N
All	23.3 % (899 of 3858)	18.9 % (377 of 1996)	20.9 % (315 of 1506)	58.1 % (207 of 356)
Backbone	36.7 % (729 of 1984)	35.8 % (246 of 688)	28.2 % (276 of 980)	65.5 % (207 of 316)
Sidechain	9.7 % (212 of 2178)	10.1 % (132 of 1308)	9.6 % (80 of 830)	0.0 % (0 of 40)
Aromatic	0.9 % (2 of 228)	1.8 % (2 of 114)	0.0 % (0 of 112)	0.0 % (0 of 2)
Methyl	13.2 % (58 of 440)	14.1 % (31 of 220)	12.3 % (27 of 220)

1. entity 1

GRKLLTYQVK QGDTLNSIAA DFRISTAALL QANPSLQAGL TAGQSIVIPG LPDPYTIPYH IAVSIGAKTL TLSLNNRVMK TYPIAVGKIL TQTPTGEFYI INRQRNPGGP FGAYWLSLSK QHYGIHGTNN PASIGKAVSK GCIRMHNKDV IELASIVPNG TRVTINRGS

Show sample condition

Sample #1

Solvent system 50 mM HEPES, pH 7.2, Pressure 1 atm, Temperature 298 (±0.2) K, pH 7.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N; U-2H]		2.5 mg/mL
2	entity_2	natural abundance		3 mg/mL
3	HEPES	natural abundance		50 mM

Sample #2

Solvent system 50 mM HEPES, pH 7.2, Pressure 1 atm, Temperature 298 (±0.2) K, pH 7.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]		376 uM
5	HEPES	natural abundance		50 mM

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Calculated from 5 models in PDB: 2MTZ, Strand ID: A Detail

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Release date

2016-06-28

Citation

Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan
Schanda, P., Triboulet, S., Laguri, C., Bougault, C., Ayala, I., Callon, M., Arthur, M., Simorre, J.
J. Am. Chem. Soc. (2014), 136, 17852-17860, PubMed 25429710 , DOI 10.1021/ja5105987 , Abstract

Related entities 1. L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide, entity 1, : 1 : 2 : 1 : 17 entities Detail

Experiments performed 4 experiments Detail