BMRB: 34255

Structure of the UB2H domain of E.coli PBP1B in complex with LpoB

Authors

Simorre, J.P., Maya Martinez, R.C., Bougault, C.

Assembly

Penicillin-binding protein 1B (E.C.2.4.1.129,3.4.16.4)

Entity

1. Penicillin-binding protein 1B (E.C.2.4.1.129,3.4.16.4) (polymer, Thiol state: not present), 114 monomers, 13160.78 Da Detail

MGSSHHHHHH SSGLVPRGSH MGRMVNLEPD MTISKNEMVK LLEATQYRQV SKMTRPGEFT VQANSIEMIR RPFDFPDSKE GQVRARLTFD GDHLATIVNM ENNRQFGFFR LDPR

Formula weight

13160.78 Da

Source organism

Escherichia coli K-12

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 82.5 %, Completeness: 67.7 %, Completeness (bb): 72.3 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	67.7 % (908 of 1341)	63.7 % (450 of 706)	73.8 % (381 of 516)	64.7 % (77 of 119)
Backbone	72.3 % (486 of 672)	69.6 % (160 of 230)	74.6 % (249 of 334)	71.3 % (77 of 108)
Sidechain	65.4 % (507 of 775)	60.9 % (290 of 476)	75.3 % (217 of 288)	0.0 % (0 of 11)
Aromatic	60.0 % (66 of 110)	60.0 % (33 of 55)	60.0 % (33 of 55)
Methyl	87.0 % (80 of 92)	89.1 % (41 of 46)	84.8 % (39 of 46)

1. entity 1

MGSSHHHHHH SSGLVPRGSH MGRMVNLEPD MTISKNEMVK LLEATQYRQV SKMTRPGEFT VQANSIEMIR RPFDFPDSKE GQVRARLTFD GDHLATIVNM ENNRQFGFFR LDPR

Show sample condition

Sample #1

Solvent system 90% H2O and 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.5, Details 400 uM [U-13C; U-15N] UB2H domain, 480 uM None LpoB, 90% H2O and 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	UB2H domain	[U-13C; U-15N]		400 (±5.0) uM
2	LpoB	natural abundance		480 (±5.0) uM
3	Tris.HCl	natural abundance		10 mM
4	NaCl	natural abundance		200 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.5, Details 450 uM [U-15N] UB2H, 540 uM None LpoB, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
5	LpoB	natural abundance		540 uM
6	UB2H	[U-15N]		450 (±5.0) uM
7	Tris.HCl	natural abundance		10 mM
8	NaCl	natural abundance		200 mM

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LACS Plot; CA

Referencing offset: -0.19 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.19 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

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LACS Plot; HA

Referencing offset: -0.06 ppm, Outliers: 3 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

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LACS Plot; CO

Referencing offset: -0.05 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

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Protein Blocks Logo

Calculated from 20 models in PDB: 6G5R, Strand ID: A Detail

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Release date

2019-03-12

Citation 1

Structural Insights into Inhibition of Escherichia coli Penicillin-binding Protein 1B
King, D.T., Wasney, G.A., Nosella, M., Fong, A., Strynadka, N.C.
J. Biol. Chem. (2017), 292, 979-993, PubMed 27899450 , DOI 10.1074/jbc.M116.718403 , Abstract

Show more 1 citaion

Citation 2

Induced conformational changes activate the peptidoglycan synthase PBP1B
Egan, A.J.F., Maya-Martinez, R., Ayala, I., Bougault, C.M., Banzhaf, M., Breukink, E., Vollmer, W., Simorre, J.P.
Mol. Microbiol. (2018), 110, 335-356, PubMed 30044025 , DOI 10.1111/mmi.14082 , Abstract

Hide non-primary 1 citaion

Related entities 1. Penicillin-binding protein 1B (E.C.2.4.1.129,3.4.16.4), : 1 : 1 : 9 : 18 entities Detail

Interaction partners 1. Penicillin-binding protein 1B (E.C.2.4.1.129,3.4.16.4), : 10 interactors Detail

Experiments performed 12 experiments Detail