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BMRB: 17767

2LFO

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

Authors

Tomaselli, S., Cogliati, C., Pagano, K., Zetta, L., Zanzoni, S., Assfalg, M., Molinari, H., Ragona, L.

Assembly

cl-BABP/SS complex

Entity

1. cl BABP (polymer, Thiol state: all disulfide bound), 125 monomers, 14081.03 Da Detail

AFSGTWQVYA QENYEEFLKA LALPEDLIKM ARDIKPIVEI QQKGDDFVVT SKTPRQTVTN SFTLGKEADI TTMDGKKLKC TVHLANGKLV CKSEKFSHEQ EVKGNEMVET ITFGGVTLIR RSKRV

2. CHO (non-polymer), 449.623 Da
3. GCH (non-polymer), 465.623 Da

Total weight

14996.276 Da

Max. entity weight

14081.03 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS80:SG	1:CYS91:SG

Source organism

Gallus gallus

Exptl. method

solution NMR

Refine. method

Molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.5 %, Completeness (bb): 95.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (1357 of 1483)	88.2 % (682 of 773)	95.1 % (549 of 577)	94.7 % (126 of 133)
Backbone	95.4 % (710 of 744)	94.9 % (242 of 255)	95.6 % (351 of 367)	95.9 % (117 of 122)
Sidechain	89.1 % (763 of 856)	84.9 % (440 of 518)	96.0 % (314 of 327)	81.8 % (9 of 11)
Aromatic	76.0 % (73 of 96)	70.8 % (34 of 48)	80.9 % (38 of 47)	100.0 % (1 of 1)
Methyl	96.6 % (141 of 146)	95.9 % (70 of 73)	97.3 % (71 of 73)

1. cl BABP

AFSGTWQVYA QENYEEFLKA LALPEDLIKM ARDIKPIVEI QQKGDDFVVT SKTPRQTVTN SFTLGKEADI TTMDGKKLKC TVHLANGKLV CKSEKFSHEQ EVKGNEMVET ITFGGVTLIR RSKRV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
2	Glycochenodeoxycholic acid	natural abundance	0.5 mM
3	glycocholic acid	natural abundance	0.75 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	sodium phosphate	natural abundance	30 mM
7	NaN3	natural abundance	0.03 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
8	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
9	Glycochenodeoxycholic acid	natural abundance	0.5 mM
10	glycocholic acid	natural abundance	0.75 mM
11	D2O	natural abundance	100 %
12	sodium phosphate	natural abundance	30 mM
13	NaN3	natural abundance	0.03 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
14	cl_BABP	[U-99% 15N]	0.5 mM
15	Glycochenodeoxycholic acid	natural abundance	0.5 mM
16	Glycocholic acid	natural abundance	0.75 mM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %
19	sodium phosphate	natural abundance	30 mM
20	NaN3	natural abundance	0.03 %

LACS Plot; CA

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

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.23 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.38 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LFO, Strand ID: A Detail

Release date

2012-03-26

Citation

A disulfide bridge allows for site-selective binding in liver bile acid binding protein thereby stabilising the orientation of key amino acid side chains
Tomaselli, S., Assfalg, M., Pagano, K., Cogliati, C., Zanzoni, S., Molinari, H., Ragona, L.
Chemistry (2012), 18, 2857-2866, PubMed 22298334 , DOI 10.1002/chem.201102203 , Abstract

Related entities 1. cl BABP, : 1 : 9 : 212 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
14	cl_BABP	[U-99% 15N]	0.5 mM
15	Glycochenodeoxycholic acid	natural abundance	0.5 mM
16	Glycocholic acid	natural abundance	0.75 mM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %
19	sodium phosphate	natural abundance	30 mM
20	NaN3	natural abundance	0.03 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
2	Glycochenodeoxycholic acid	natural abundance	0.5 mM
3	glycocholic acid	natural abundance	0.75 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	sodium phosphate	natural abundance	30 mM
7	NaN3	natural abundance	0.03 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
2	Glycochenodeoxycholic acid	natural abundance	0.5 mM
3	glycocholic acid	natural abundance	0.75 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	sodium phosphate	natural abundance	30 mM
7	NaN3	natural abundance	0.03 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
2	Glycochenodeoxycholic acid	natural abundance	0.5 mM
3	glycocholic acid	natural abundance	0.75 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	sodium phosphate	natural abundance	30 mM
7	NaN3	natural abundance	0.03 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
8	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
9	Glycochenodeoxycholic acid	natural abundance	0.5 mM
10	glycocholic acid	natural abundance	0.75 mM
11	D2O	natural abundance	100 %
12	sodium phosphate	natural abundance	30 mM
13	NaN3	natural abundance	0.03 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
14	cl_BABP	[U-99% 15N]	0.5 mM
15	Glycochenodeoxycholic acid	natural abundance	0.5 mM
16	Glycocholic acid	natural abundance	0.75 mM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %
19	sodium phosphate	natural abundance	30 mM
20	NaN3	natural abundance	0.03 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
2	Glycochenodeoxycholic acid	natural abundance	0.5 mM
3	glycocholic acid	natural abundance	0.75 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	sodium phosphate	natural abundance	30 mM
7	NaN3	natural abundance	0.03 %

8 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
2	Glycochenodeoxycholic acid	natural abundance	0.5 mM
3	glycocholic acid	natural abundance	0.75 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	sodium phosphate	natural abundance	30 mM
7	NaN3	natural abundance	0.03 %

9 3D F1-[13C]-filtered, F2-[13C]-separated, F3-[15N,13C]-edited NOESY-HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
8	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
9	Glycochenodeoxycholic acid	natural abundance	0.5 mM
10	glycocholic acid	natural abundance	0.75 mM
11	D2O	natural abundance	100 %
12	sodium phosphate	natural abundance	30 mM
13	NaN3	natural abundance	0.03 %

10 F1/F2-[15N,13C]-filtered NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
8	cl_BABP	[U-99% 13C; U-99% 15N]	0.5 mM
9	Glycochenodeoxycholic acid	natural abundance	0.5 mM
10	glycocholic acid	natural abundance	0.75 mM
11	D2O	natural abundance	100 %
12	sodium phosphate	natural abundance	30 mM
13	NaN3	natural abundance	0.03 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17767_2lfo.nef
Input source #2: Coordindates	2lfo.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	None
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:80:CYS:SG	A:91:CYS:SG	oxidized, CA 56.5, CB 45.7 ppm	oxidized, CA 55.23, CB 42.97 ppm	2.029

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CHO	GLYCOCHENODEOXYCHOLIC ACID	Distance restraints
C	1	GCH	GLYCOCHOLIC ACID	Distance restraints

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
AFSGTWQVYAQENYEEFLKALALPEDLIKMARDIKPIVEIQQKGDDFVVTSKTPRQTVTNSFTLGKEADITTMDGKKLKCTVHLANGKLVCKSEKFSHEQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AFSGTWQVYAQENYEEFLKALALPEDLIKMARDIKPIVEIQQKGDDFVVTSKTPRQTVTNSFTLGKEADITTMDGKKLKCTVHLANGKLVCKSEKFSHEQ

-------110-------120-----
EVKGNEMVETITFGGVTLIRRSKRV
|||||||||||||||||||||||||
EVKGNEMVETITFGGVTLIRRSKRV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_17767_2lfo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1354		100.0 (chain: A, length: 125)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	108 (1)	undefined	16.0 (chain: A, length: 125), 100.0 (chain: B, length: 1), 100.0 (chain: C, length: 1)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	2959 (1)	noe	99.2 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 677
  - ¹³C chemical shifts: 548
  - ¹⁵N chemical shifts: 129
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
83	HIS	ND1	207.7
83	HIS	NE2	197.6
98	HIS	HE2	11.5
98	HIS	ND1	257.7
98	HIS	NE2	167.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	773	676	87.5
¹³C chemical shifts	577	548	95.0
¹⁵N chemical shifts	138	125	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	255	247	96.9
¹³C chemical shifts	250	237	94.8
¹⁵N chemical shifts	122	116	95.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	518	429	82.8
¹³C chemical shifts	327	311	95.1
¹⁵N chemical shifts	16	9	56.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	73	96.1
¹³C chemical shifts	76	73	96.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	30	62.5
¹³C chemical shifts	47	36	76.6
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 16.0%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 105
- Weight of restraints: 1.0 (105)
- Potential type of restraints: square-well-parabolic (105)
- Range of distance target values: 3.25, 5.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 99.2%
  - Total number of restraints: 2959
  - Weight of restraints: 1.0 (2959)
  - Potential type of restraints: square-well-parabolic (2959)
  - Range of distance target values: 2.21, 3.78 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
    - Chain_ID: C
      None
  - Distance restraints on contact map

Keywords bile acid binding protein, bile acids, heterotypic complex, liver

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Found 1 Document (0.747 seconds)

BMRB: 17767

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. cl BABP, : 1 : 9 : 212 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 4 contents Detail