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BMRB: 17551

2LBA

Solution structure of chicken ileal BABP in complex with glycochenodeoxycholic acid

Authors

Zanzoni, S., Assfalg, M., Giorgetti, A., D'Onofrio, M., Molinari, H.

Assembly

cI-BABP-GCDA complex

Entity

1. Protein (polymer, Thiol state: all free), 127 monomers, 14123.72 Da Detail

AFTGKYEFES DENYDDFVKK IGLPADKIEM GRNCKIVTEV VQNGNDFTWT QHFPGGRTTT NSFTIDKEAD METMGGRKFK ATVKMEGGKI VADFPNYHHT AEISGGKLVE ISTSSGVVYK RTSKKIA

2. CHO (non-polymer, Thiol state: not present), 449.623 × 2 Da

Total weight

15022.966 Da

Max. entity weight

14123.72 Da

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: 91.3 %, Completeness (bb): 98.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.3 % (1337 of 1465)	95.8 % (728 of 760)	83.9 % (480 of 572)	97.0 % (129 of 133)
Backbone	98.3 % (743 of 756)	99.2 % (262 of 264)	97.3 % (358 of 368)	99.2 % (123 of 124)
Sidechain	85.4 % (703 of 823)	94.0 % (466 of 496)	72.6 % (231 of 318)	66.7 % (6 of 9)
Aromatic	45.6 % (62 of 136)	89.7 % (61 of 68)	0.0 % (0 of 67)	100.0 % (1 of 1)
Methyl	99.1 % (115 of 116)	100.0 % (58 of 58)	98.3 % (57 of 58)

1. Protein

AFTGKYEFES DENYDDFVKK IGLPADKIEM GRNCKIVTEV VQNGNDFTWT QHFPGGRTTT NSFTIDKEAD METMGGRKFK ATVKMEGGKI VADFPNYHHT AEISGGKLVE ISTSSGVVYK RTSKKIA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Protein	natural abundance	0.4 mM
2	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	1.6 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	phosphate buffer	natural abundance	30 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
7	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %
10	phosphate buffer	natural abundance	30 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
12	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
13	D2O	natural abundance	100 %
14	phosphate buffer	natural abundance	30 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl protons	external	indirect	0.2514495
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	TSP	methyl protons	external	indirect	0.101329

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl protons	external	indirect	0.2514495
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	TSP	methyl protons	external	indirect	0.101329

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl protons	external	indirect	0.2514495
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	TSP	methyl protons	external	indirect	0.101329

Referencing offset: -0.18 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl protons	external	indirect	0.2514495
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	TSP	methyl protons	external	indirect	0.101329

Referencing offset: 0.48 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2012-05-09

Citation

Structural requirements for cooperativity in ileal bile acid-binding proteins
Zanzoni, S., Assfalg, M., Giorgetti, A., Molinari, M.
J. Biol. Chem. (2011), 286, 39307-39317, PubMed 21917914 , DOI 10.1074/jbc.M111.261099 , Abstract

Related entities 1. Protein, : 1 : 226 entities Detail

Experiments performed 8 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 6.5

#	Name	Isotope labeling	Concentration
6	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
7	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %
10	phosphate buffer	natural abundance	30 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
12	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
13	D2O	natural abundance	100 %
14	phosphate buffer	natural abundance	30 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Protein	natural abundance	0.4 mM
2	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	1.6 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	phosphate buffer	natural abundance	30 mM

4 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
12	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
13	D2O	natural abundance	100 %
14	phosphate buffer	natural abundance	30 mM

5 3D H(C)CH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
12	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
13	D2O	natural abundance	100 %
14	phosphate buffer	natural abundance	30 mM

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 6.5

#	Name	Isotope labeling	Concentration
6	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
7	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %
10	phosphate buffer	natural abundance	30 mM

7 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
7	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %
10	phosphate buffer	natural abundance	30 mM

8 3D 13C-edited 13C-filtered NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	Protein	[U-100% 13C; U-100% 15N]	0.8 mM
12	GLYCOCHENODEOXYCHOLIC ACID	natural abundance	3.2 mM
13	D2O	natural abundance	100 %
14	phosphate buffer	natural abundance	30 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17551_2lba.nef
Input source #2: Coordindates	2lba.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

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
B	2	CHO	GLYCOCHENODEOXYCHOLIC ACID	None

Sequence alignments

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

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

--100-------110-------120-------130-
NYHHTAEISGGKLVEISTSSGVVYKRTSKKIALVPR
||||||||||||||||||||||||||||||||||||
NYHHTAEISGGKLVEISTSSGVVYKRTSKKIALVPR
-------110-------120-------130------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	136	0	0	100.0

Content subtype: combined_17551_2lba.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1321		93.4 (chain: A, length: 136)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	3533 (1)	noe	93.4 (chain: A, length: 136)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Error	28 (1)	undefined	11.0 (chain: A, length: 136), 50.0 (chain: B, length: 2)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	219 (219)	.	93.4 (chain: A, length: 136)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 93.4%
- Total number of assignments
  - ¹H chemical shifts: 720
  - ¹³C chemical shifts: 472
  - ¹⁵N chemical shifts: 129
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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)
99	HIS	HE2	12.007

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	818	719	87.9
¹³C chemical shifts	613	472	77.0
¹⁵N chemical shifts	147	129	87.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	282	262	92.9
¹³C chemical shifts	272	246	90.4
¹⁵N chemical shifts	132	123	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	536	457	85.3
¹³C chemical shifts	341	226	66.3
¹⁵N chemical shifts	15	6	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	62	91.2
¹³C chemical shifts	68	61	89.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	61	89.7
¹³C chemical shifts	67	0	0.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 93.4%
- Total number of restraints: 3522
- Weight of restraints: 1.0 (3522)
- Potential type of restraints: upper-bound-parabolic (3522)
- Range of distance target values: 2.3, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Error
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 11.0%
    - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
  - Total number of restraints: 28
  - Weight of restraints: 1.0 (28)
  - Potential type of restraints: square-well-parabolic (28)
  - Range of distance target values: 4.0, 4.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 93.4%
- Total number of restraints: 219
- Total number of restraints per polymer type: 219
- Weight of restraints: 1.0 (219)
- Potential type of restraints: square-well-parabolic (219)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Bile Acid Binding Protein, Glycochenodeoxycholic acid, intracellular lipid binding protein

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Found 1 Document (0.948 seconds)

BMRB: 17551

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Protein, : 1 : 226 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 5 contents Detail