BMRB Entry 19681

Name: NMR structure of E. coli LpoB
Published: 2014-04-11

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PDB ID: 2mii
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19681
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of E. coli LpoB

Deposition date:

2013-12-13

Original release date:

2014-04-11

Authors:

Egan, Alexander; Jean, Nicolas; Koumoutsi, Alexandra; Bougault, Catherine; Biboy, Jacob; Sassine, Jad; Solovyova, Alexandra; Breukink, Eefjan; Typas, Athanasios; Vollmer, Waldemar; Simorre, Jean-Pierre

Citation:

Citation: Jean, Nicolas; Bougault, Catherine; Egan, Alexander; Vollmer, Waldemar; Simorre, Jean-Pierre. "Solution NMR assignment of LpoB, an outer-membrane anchored Penicillin-Binding Protein activator from Escherichia coli." Biomol. NMR Assignments ., .-. (2014).
PubMed: 24691651

Assembly members:

Assembly members:
LpoB, polymer, 197 residues, 20770.459 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28LpoB

Entity Sequences (FASTA):

Entity Sequences (FASTA):
LpoB: GSHMVGQREPAPVEEVKPAP EQPAEPQQPVPTVPSVPTIP QQPGPIEHEDQTAPPAPHIR HYDWNGAMQPMVSKMLGADG VTAGSVLLVDSVNNRTNGSL NAAEATETLRNALANNGKFT LVSAQQLSMAKQQLGLSPQD SLGTRSKAIGIARNVGAHYV LYSSASGNVNAPTLQMQLML VQTGEIIWSGKGAVSQQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list

Data type	Count
13C chemical shifts	756
15N chemical shifts	197
1H chemical shifts	1165

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	E. coli LpoB	1

Entities:

Entity 1, E. coli LpoB 197 residues - 20770.459 Da.

Residues 1 to 4 are reminiscent of the hexahistidine-tag left after thrombine cleavage

1

GLY

SER

HIS

MET

VAL

GLY

GLN

ARG

GLU

PRO

2

ALA

PRO

VAL

GLU

VAL

LYS

PRO

ALA

PRO

3

GLU

GLN

PRO

ALA

GLU

PRO

GLN

PRO

VAL

4

PRO

THR

VAL

PRO

SER

VAL

PRO

THR

ILE

PRO

5

GLN

PRO

GLY

PRO

ILE

GLU

HIS

GLU

ASP

6

GLN

THR

ALA

PRO

ALA

PRO

HIS

ILE

ARG

7

HIS

TYR

ASP

TRP

ASN

GLY

ALA

MET

GLN

PRO

8

MET

VAL

SER

LYS

MET

LEU

GLY

ALA

ASP

GLY

9

VAL

THR

ALA

GLY

SER

VAL

LEU

VAL

ASP

10

SER

VAL

ASN

ARG

THR

ASN

GLY

SER

LEU

11

ASN

ALA

GLU

ALA

THR

GLU

THR

LEU

ARG

12

ASN

ALA

LEU

ALA

ASN

GLY

LYS

PHE

THR

13

LEU

VAL

SER

ALA

GLN

LEU

SER

MET

ALA

14

LYS

GLN

LEU

GLY

LEU

SER

PRO

GLN

ASP

15

SER

LEU

GLY

THR

ARG

SER

LYS

ALA

ILE

GLY

16

ILE

ALA

ARG

ASN

VAL

GLY

ALA

HIS

TYR

VAL

17

LEU

TYR

SER

ALA

SER

GLY

ASN

VAL

ASN

18

ALA

PRO

THR

LEU

GLN

MET

GLN

LEU

MET

LEU

19

VAL

GLN

THR

GLY

GLU

ILE

TRP

SER

GLY

20

LYS

GLY

ALA

VAL

SER

GLN

Samples:

LpoB(sol): LpoB, [U-100% 13C; U-100% 15N], 0.8 mM; CH3COOH/CH3COONa buffer 100.0 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 0.100 M; pH: 5.000; pressure: 1.000 atm; temperature: 308.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	LpoB(sol)	isotropic	sample_conditions_1
3D HNCO	LpoB(sol)	isotropic	sample_conditions_1
3D HN(CA)CO	LpoB(sol)	isotropic	sample_conditions_1
3D BEST-HNCACB	LpoB(sol)	isotropic	sample_conditions_1
3D BEST-HN(CO)CACB	LpoB(sol)	isotropic	sample_conditions_1
3D HN(COCA)N(H)	LpoB(sol)	isotropic	sample_conditions_1
2D Pro-HN(COCAN)	LpoB(sol)	isotropic	sample_conditions_1
2D Pro-iHN(CAN)	LpoB(sol)	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	LpoB(sol)	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	LpoB(sol)	isotropic	sample_conditions_1
2D methyl 1H-13C-CT-HSQC	LpoB(sol)	isotropic	sample_conditions_1
2D 1H-15N HMQC optimized for His sidechains	LpoB(sol)	isotropic	sample_conditions_1
3D H(C)CH-TOCSY	LpoB(sol)	isotropic	sample_conditions_1
3D H(CCO)NH	LpoB(sol)	isotropic	sample_conditions_1
3D C(CO)NH	LpoB(sol)	isotropic	sample_conditions_1
3D 1H-15N NOESY	LpoB(sol)	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	LpoB(sol)	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	LpoB(sol)	isotropic	sample_conditions_1
3D methyl 1H-13C NOESY	LpoB(sol)	isotropic	sample_conditions_1
Heteronuclear 1H-15N NOE	LpoB(sol)	isotropic	sample_conditions_1

Software:

Aria v2.3.1, Linge, O'Donoghue and Nilges - structure calculation

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - Refinement

CcpNmr_Analysis v2.2, CCPN - data analysis

Talos+, Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Bax - data analysis

Unio10' v2.0.2, Torsten Herrmann - peakpicking

nmrDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

nmrPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian vnmrs 800 MHz
Varian vnmrs 600 MHz
Bruker US2 950 MHz

UNP	P0AB38
PDB	2MII 4Q6Z
DBJ	BAA35912 BAB34906 BAG76694 BAI24739 BAI29989
EMBL	CAP75597 CAQ31626 CAQ98004 CAR02445 CAR07449
GB	AAC74189 AAG55851 AAN79848 AAP16615 AAZ87850
REF	NP_309510 NP_415623 WP_000164436 WP_000164438 WP_000164439
SP	P0AB38 P0AB39 Q3Z312
AlphaFold	Q9R424 P0AB38 P0AB39 Q3Z312