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Found 1 Document (0.849 seconds)

BMRB: 15084

2JN3

NMR structure of cl-BABP complexed to chenodeoxycholic acid

Authors

Eliseo, T., Ragona, L., Catalano, M., Assfalf, M., Paci, M., Zetta, L., Molinari, H., Cicero, D.O.

Assembly

CDA-BABP complex

Entity

1. cl-BABP (polymer, Thiol state: all free), 125 monomers, 14078.99 Da Detail

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

2. JN3 (non-polymer), 392.572 × 2 Da

Total weight

14864.134 Da

Max. entity weight

14078.99 Da

Source organism

Gallus gallus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.2 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.2 % (1428 of 1484)	95.7 % (740 of 773)	98.4 % (569 of 578)	89.5 % (119 of 133)
Backbone	98.8 % (735 of 744)	98.0 % (250 of 255)	99.7 % (366 of 367)	97.5 % (119 of 122)
Sidechain	94.5 % (810 of 857)	94.6 % (490 of 518)	97.6 % (320 of 328)	0.0 % (0 of 11)
Aromatic	92.7 % (89 of 96)	97.9 % (47 of 48)	89.4 % (42 of 47)	0.0 % (0 of 1)
Methyl	99.3 % (147 of 148)	100.0 % (74 of 74)	98.6 % (73 of 74)

1. cl-BABP

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

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
6	CDA	natural abundance	3 mM
7	H2O		100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
9	CDA	natural abundance	3 mM
10	H2O		90 %
11	D2O		10 %

LACS Plot; CA

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

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.18 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.72 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JN3, Strand ID: A Detail

Release date

2008-02-10

Citation

Structural and dynamic determinants of ligand binding in the ternary complex of chicken liver bile acid binding protein with two bile salts revealed by NMR
Eliseo, T., Ragona, L., Catalano, M., Assfalf, M., Paci, M., Zetta, L., Molinari, H., Cicero, D.O.
Biochemistry (2007), 46, 12557-12567, PubMed 17929837 , DOI 10.1021/bi7013085 , Abstract

Related entities 1. cl-BABP, : 1 : 8 : 1 : 220 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

2 3D HNCO

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

3 3D HNCA

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 400 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

6 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
6	CDA	natural abundance	3 mM
7	H2O		100 %

7 3D H(C)CH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
6	CDA	natural abundance	3 mM
7	H2O		100 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

9 3D 1H-15N TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

11 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
2	CDA	natural abundance	3 mM
3	H2O		90 %
4	D2O		10 %

12 3D 13C-edited 13C-filtered NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	cl-BABP	[U-100% 13C; U-100% 15N]	1.2 mM
6	CDA	natural abundance	3 mM
7	H2O		100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15084_2jn3.nef
Input source #2: Coordindates	2jn3.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	JN3	CHENODEOXYCHOLIC ACID	Distance restraints
B	2	JN3	CHENODEOXYCHOLIC ACID	None

Sequence alignments

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

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

-------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_15084_2jn3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1463		100.0 (chain: A, length: 125)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	1622 (1)	noe	100.0 (chain: A, length: 125)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Error	219 (1)	undefined	24.8 (chain: A, length: 125), 50.0 (chain: B, length: 2)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	152 (1)	hbond	70.4 (chain: A, length: 125), 50.0 (chain: B, length: 2)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	230 (230)	.	99.2 (chain: A, length: 125)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_2	OK	459 (459)	.	96.8 (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%

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

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

Total number of assignments
- ¹H chemical shifts: 744
- ¹³C chemical shifts: 596
- ¹⁵N chemical shifts: 123

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
7	GLN	CD	179.24
11	GLN	CD	177.2
12	GLU	CD	182.9
13	ASN	CG	178.59
15	GLU	CD	183.04
16	GLU	CD	183.54
25	GLU	CD	183.23
26	ASP	CG	179.28
33	ASP	CG	180.23
39	GLU	CD	183.16
41	GLN	CD	180.01
42	GLN	CD	179.1
45	ASP	CG	179.8
46	ASP	CG	180.2
56	GLN	CD	179.6
60	ASN	CG	176.5
67	GLU	CD	183.51
69	ASP	CG	180.6
74	ASP	CG	179.43
83	HIS	ND1	218.1
83	HIS	NE2	184.7
86	ASN	CG	178.0
94	GLU	CD	183.7
98	HIS	ND1	253.0
98	HIS	NE2	162.2
99	GLU	CD	183.46
100	GLN	CD	176.5
101	GLU	CD	182.51
105	ASN	CG	177.54
106	GLU	CD	183.216
109	GLU	CD	183.05

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	773	744	96.2
¹³C chemical shifts	578	569	98.4
¹⁵N chemical shifts	138	119	86.2

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	255	253	99.2
¹³C chemical shifts	250	249	99.6
¹⁵N chemical shifts	122	119	97.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	518	491	94.8
¹³C chemical shifts	328	320	97.6
¹⁵N chemical shifts	16	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	77	100.0
¹³C chemical shifts	77	76	98.7

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	47	97.9
¹³C chemical shifts	47	42	89.4
¹⁵N chemical shifts	1	0	0.0

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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 100.0%
- Total number of restraints: 1622
- Weight of restraints: 1.0 (1622)
- Potential type of restraints: square-well-parabolic (1622)
- Range of distance target values: 2.4, 4.65 (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_6
  - Status: Error
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 24.8%
    - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
  - Total number of restraints: 219
  - Weight of restraints: 1.0 (219)
  - Potential type of restraints: square-well-parabolic (219)
  - Range of distance target values: 2.75, 5.75 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 70.4%
      - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
    - Total number of restraints: 152
    - Weight of restraints: 1.0 (152)
    - Potential type of restraints: square-well-parabolic (152)
    - Range of distance target values: 1.57, 4.31 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 99.2%
- Total number of restraints: 230
- Total number of restraints per polymer type: 230
- Weight of restraints: 1.0 (230)
- Potential type of restraints: square-well-parabolic (230)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 96.8%
- Total number of restraints: 459
- Potential type of restraints: undefined (459)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords bile acid, binding, chenodeoxycholic, NMR, BILE ACIDS, BINDING

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Found 1 Document (0.849 seconds)

BMRB: 15084

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. cl-BABP, : 1 : 8 : 1 : 220 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 7 contents Detail