BMRB Entry 17767

Name: NMR structure of cl-BABP/SS complexed with glycochenodeoxycholic and glycocholic acids
Published: 2012-03-27

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PDB ID: 2lfo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17767
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of cl-BABP/SS complexed with glycochenodeoxycholic and glycocholic acids

Deposition date:

2011-07-07

Original release date:

2012-03-27

Authors:

Tomaselli, Simona; Cogliati, Clelia; Pagano, Katiuscia; Zetta, Lucia; Zanzoni, Serena; Assfalg, Michael; Molinari, Henriette; Ragona, Laura

Citation:

Citation: Tomaselli, Simona; Assfalg, Michael; Pagano, Katiuscia; Cogliati, Clelia; Zanzoni, Serena; Molinari, Henriette; Ragona, Laura. "A disulfide bridge allows for site-selective binding in liver bile Acid binding protein thereby stabilising the orientation of key amino Acid side chains." Chemistry 18, 2857-2866 (2012).
PubMed: 22298334

Assembly members:

Assembly members:
cl_BABP, polymer, 125 residues, 14102.333 Da.
CHO, non-polymer, 449.623 Da.
GCH, non-polymer, 465.623 Da.

Natural source:

Natural source: Common Name: chicken Taxonomy ID: 9031 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Gallus gallus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PET24D

Entity Sequences (FASTA):

Entity Sequences (FASTA):
cl_BABP: AFSGTWQVYAQENYEEFLKA LALPEDLIKMARDIKPIVEI QQKGDDFVVTSKTPRQTVTN SFTLGKEADITTMDGKKLKC TVHLANGKLVCKSEKFSHEQ EVKGNEMVETITFGGVTLIR RSKRV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	548
15N chemical shifts	129
1H chemical shifts	823

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	cl_BABP	1
2	6-(3',5'-DIMETHYLBENZYL)-1-ETHOXYMETHYL-5-ISOPROPYLURACIL	2
3	SUGAR (4,5-DEHYDRO-D-GLUCURONIC ACID)	3

Entities:

Entity 1, cl_BABP 125 residues - 14102.333 Da.

1

ALA

PHE

SER

GLY

THR

TRP

GLN

VAL

TYR

ALA

2

GLN

GLU

ASN

TYR

GLU

PHE

LEU

LYS

ALA

3

LEU

ALA

LEU

PRO

GLU

ASP

LEU

ILE

LYS

MET

4

ALA

ARG

ASP

ILE

LYS

PRO

ILE

VAL

GLU

ILE

5

GLN

LYS

GLY

ASP

PHE

VAL

THR

6

SER

LYS

THR

PRO

ARG

GLN

THR

VAL

THR

ASN

7

SER

PHE

THR

LEU

GLY

LYS

GLU

ALA

ASP

ILE

8

THR

MET

ASP

GLY

LYS

LEU

LYS

CYS

9

THR

VAL

HIS

LEU

ALA

ASN

GLY

LYS

LEU

VAL

10

CYS

LYS

SER

GLU

LYS

PHE

SER

HIS

GLU

GLN

11

GLU

VAL

LYS

GLY

ASN

GLU

MET

VAL

GLU

THR

12

ILE

THR

PHE

GLY

VAL

THR

LEU

ILE

ARG

13

ARG

SER

LYS

ARG

VAL

Entity 2, 6-(3',5'-DIMETHYLBENZYL)-1-ETHOXYMETHYL-5-ISOPROPYLURACIL - C26 H43 N O5 - 449.623 Da.

1

CHO

Entity 3, SUGAR (4,5-DEHYDRO-D-GLUCURONIC ACID) - C26 H43 N O6 - 465.623 Da.

1

GCH

Samples:

sample_1: cl_BABP, [U-99% 13C; U-99% 15N], 0.5 mM; Glycochenodeoxycholic acid 0.5 mM; glycocholic acid 0.75 mM; H2O 90%; D2O 10%; sodium phosphate 30 mM; NaN3 0.03%

sample_2: cl_BABP, [U-99% 13C; U-99% 15N], 0.5 mM; Glycochenodeoxycholic acid 0.5 mM; glycocholic acid 0.75 mM; D2O 100%; sodium phosphate 30 mM; NaN3 0.03%

sample_3: cl_BABP, [U-99% 15N], 0.5 mM; Glycochenodeoxycholic acid 0.5 mM; Glycocholic acid 0.75 mM; H2O 90%; D2O 10%; sodium phosphate 30 mM; NaN3 0.03%

sample_conditions_1: ionic strength: 30 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D F1-[13C]-filtered, F2-[13C]-separated, F3-[15N,13C]-edited NOESY-HSQC	sample_2	isotropic	sample_conditions_1
F1/F2-[15N,13C]-filtered NOESY	sample_2	isotropic	sample_conditions_1

Software:

X-PLOR NIH v2.26, Schwieters, Kuszewski, Tjandra and Clore - structure solution

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz
Bruker DMX 500 MHz
Bruker Avance 900 MHz

BMRB	15084 15854 16309 16310 16458
PDB	1MVG 1TVQ 1TW4 1ZRY 2JN3 2K62 2LFO
GB	AAK58094 ADE59142 ADE59143 ADE59144 ADE59145
PRF	2106165A
REF	NP_989965 XP_003212677
SP	P80226
AlphaFold	P80226