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Found 1 Document (0.695 seconds)

BMRB: 15434

2JU8

Solution-State Structures of Oleate-Liganded LFABP, Major Form of 1:2 Protein-Ligand Complex

Authors

He, Y., Yang, X., Wang, H., Estephan, R., Francis, F., Kodukula, S., Storch, J., Stark, R.E.

Assembly

cpxLFABP

Entity

1. LFABP (polymer, Thiol state: not reported), 127 monomers, 14272.36 Da Detail

MNFSGKYQVQ SQENFEPFMK AMGLPEDLIQ KGKDIKGVSE IVHEGKKVKL TITYGSKVIH NEFTLGEECE LETMTGEKVK AVVKMEGDNK MVTTFKGIKS VTEFNGDTIT NTMTLGDIVY KRVSKRI

2. OLA (non-polymer), 282.461 × 2 Da

Total weight

14837.282 Da

Max. entity weight

14272.36 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.7 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.7 % (1431 of 1511)	92.0 % (727 of 790)	97.4 % (571 of 586)	98.5 % (133 of 135)
Backbone	98.8 % (749 of 758)	98.5 % (260 of 264)	99.2 % (366 of 369)	98.4 % (123 of 125)
Sidechain	91.7 % (796 of 868)	88.8 % (467 of 526)	96.1 % (319 of 332)	100.0 % (10 of 10)
Aromatic	87.0 % (80 of 92)	87.0 % (40 of 46)	87.0 % (40 of 46)
Methyl	97.8 % (133 of 136)	97.1 % (66 of 68)	98.5 % (67 of 68)

1. LFABP

MNFSGKYQVQ SQENFEPFMK AMGLPEDLIQ KGKDIKGVSE IVHEGKKVKL TITYGSKVIH NEFTLGEECE LETMTGEKVK AVVKMEGDNK MVTTFKGIKS VTEFNGDTIT NTMTLGDIVY KRVSKRI

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details U-13C, 15N-LFABP with 3 equivalents of unlabeled-oleate to LFABP, pD7

#	Name	Isotope labeling	Concentration
1	LFABP	[U-99% 13C; U-99% 15N]	0.7 ~ 1.0 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium azide	natural abundance	0.02 %
4	EDTA	natural abundance	5 uM
5	D2O	natural abundance	100 %
6	oleate	natural abundance	3 eq
7	sodium chloride	natural abundance	100 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details U-15N-LFABP with 3 equivalents of U-13C-oleate to LFABP, pH7

#	Name	Isotope labeling	Concentration
8	LFABP	[U-99% 15N]	0.7 ~ 1.0 mM
9	sodium phosphate	natural abundance	50 mM
10	sodium azide	natural abundance	0.02 %
11	EDTA	natural abundance	5 uM
12	D2O	natural abundance	98 %
13	oleate	[U-99% 13C]	3 eq
14	sodium chloride	natural abundance	100 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details U-13C, 15N-LFABP with 3 equivalents of unlabeled-oleate to LFABP, pH7

#	Name	Isotope labeling	Concentration
15	LFABP	[U-99% 13C; U-99% 15N]	0.7 ~ 1.0 mM
16	sodium phosphate	natural abundance	50 mM
17	sodium azide	natural abundance	0.02 %
18	EDTA	natural abundance	5 uM
19	D2O	natural abundance	5 %
20	oleate	natural abundance	3 eq
21	sodium chloride	natural abundance	100 mM

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: -0.33 ppm, Outliers: 2 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: -0.33 ppm, Outliers: 2 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: -0.16 ppm, Outliers: 5 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: 0.44 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2JU8, Strand ID: A Detail

Release date

2007-08-15

Citation

Solution-state molecular structure of apo and oleate-liganded liver fatty acid-binding protein
He, Y., Yang, X., Wang, H., Estephan, R., Francis, F., Kodukula, S., Storch, J., Stark, R.E.
Biochemistry (2007), 46, 12543-12556, PubMed 17927211 , DOI 10.1021/bi701092r , Abstract

Related entities 1. LFABP, : 1 : 4 : 1 : 217 entities Detail

Interaction partners 1. LFABP, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 6 experiments Detail

1 3D 13C-filtered NOE

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, Details U-13C, 15N-LFABP with 3 equivalents of unlabeled-oleate to LFABP, pD7

#	Name	Isotope labeling	Concentration
1	LFABP	[U-99% 13C; U-99% 15N]	0.7 ~ 1.0 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium azide	natural abundance	0.02 %
4	EDTA	natural abundance	5 uM
5	D2O	natural abundance	100 %
6	oleate	natural abundance	3 eq
7	sodium chloride	natural abundance	100 mM

2 3D 13C-filtered NOE

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details U-15N-LFABP with 3 equivalents of U-13C-oleate to LFABP, pH7

#	Name	Isotope labeling	Concentration
8	LFABP	[U-99% 15N]	0.7 ~ 1.0 mM
9	sodium phosphate	natural abundance	50 mM
10	sodium azide	natural abundance	0.02 %
11	EDTA	natural abundance	5 uM
12	D2O	natural abundance	98 %
13	oleate	[U-99% 13C]	3 eq
14	sodium chloride	natural abundance	100 mM

3 3D 13C-filtered NOE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details U-13C, 15N-LFABP with 3 equivalents of unlabeled-oleate to LFABP, pH7

#	Name	Isotope labeling	Concentration
15	LFABP	[U-99% 13C; U-99% 15N]	0.7 ~ 1.0 mM
16	sodium phosphate	natural abundance	50 mM
17	sodium azide	natural abundance	0.02 %
18	EDTA	natural abundance	5 uM
19	D2O	natural abundance	5 %
20	oleate	natural abundance	3 eq
21	sodium chloride	natural abundance	100 mM

4 3D 13C-filtered NOE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details U-15N-LFABP with 3 equivalents of U-13C-oleate to LFABP, pH7

#	Name	Isotope labeling	Concentration
8	LFABP	[U-99% 15N]	0.7 ~ 1.0 mM
9	sodium phosphate	natural abundance	50 mM
10	sodium azide	natural abundance	0.02 %
11	EDTA	natural abundance	5 uM
12	D2O	natural abundance	98 %
13	oleate	[U-99% 13C]	3 eq
14	sodium chloride	natural abundance	100 mM

5 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details U-15N-LFABP with 3 equivalents of U-13C-oleate to LFABP, pH7

#	Name	Isotope labeling	Concentration
8	LFABP	[U-99% 15N]	0.7 ~ 1.0 mM
9	sodium phosphate	natural abundance	50 mM
10	sodium azide	natural abundance	0.02 %
11	EDTA	natural abundance	5 uM
12	D2O	natural abundance	98 %
13	oleate	[U-99% 13C]	3 eq
14	sodium chloride	natural abundance	100 mM

6 2D 1H-13C HMQC-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details U-15N-LFABP with 3 equivalents of U-13C-oleate to LFABP, pH7

#	Name	Isotope labeling	Concentration
8	LFABP	[U-99% 15N]	0.7 ~ 1.0 mM
9	sodium phosphate	natural abundance	50 mM
10	sodium azide	natural abundance	0.02 %
11	EDTA	natural abundance	5 uM
12	D2O	natural abundance	98 %
13	oleate	[U-99% 13C]	3 eq
14	sodium chloride	natural abundance	100 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15434_2ju8.nef
Input source #2: Coordindates	2ju8.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	Warning

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	OLA	OLEIC ACID	None
B	2	OLA	OLEIC 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
MNFSGKYQVQSQENFEPFMKAMGLPEDLIQKGKDIKGVSEIVHEGKKVKLTITYGSKVIHNEFTLGEECELETMTGEKVKAVVKMEGDNKMVTTFKGIKS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MNFSGKYQVQSQENFEPFMKAMGLPEDLIQKGKDIKGVSEIVHEGKKVKLTITYGSKVIHNEFTLGEECELETMTGEKVKAVVKMEGDNKMVTTFKGIKS

-------110-------120-------
VTEFNGDTITNTMTLGDIVYKRVSKRI
|||||||||||||||||||||||||||
VTEFNGDTITNTMTLGDIVYKRVSKRI

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	127	0	0	100.0

Content subtype: combined_15434_2ju8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1467		99.2 (chain: A, length: 127)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	68 (1)	hbond	37.8 (chain: A, length: 127)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	185 (185)	.	95.3 (chain: A, length: 127)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 99.2%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MNFSGKYQVQSQENFEPFMKAMGLPEDLIQKGKDIKGVSEIVHEGKKVKLTITYGSKVIHNEFTLGEECELETMTGEKVKAVVKMEGDNKMVTTFKGIKS
 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
.NFSGKYQVQSQENFEPFMKAMGLPEDLIQKGKDIKGVSEIVHEGKKVKLTITYGSKVIHNEFTLGEECELETMTGEKVKAVVKMEGDNKMVTTFKGIKS

-------110-------120-------
VTEFNGDTITNTMTLGDIVYKRVSKRI
|||||||||||||||||||||||||||
VTEFNGDTITNTMTLGDIVYKRVSKRI

Total number of assignments
- ¹H chemical shifts: 724
- ¹³C chemical shifts: 608
- ¹⁵N chemical shifts: 135

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	ASN	CG	177.6
3	PHE	CG	138.6
7	TYR	CG	131.25
7	TYR	CZ	158.081
8	GLN	CD	180.2
10	GLN	CD	179.7
12	GLN	CD	180.6
13	GLU	CD	183.6
14	ASN	CG	178.4
15	PHE	CG	138.786
16	GLU	CD	183.1
18	PHE	CG	137.76
26	GLU	CD	183.4
27	ASP	CG	179.7
30	GLN	CD	180.3
34	ASP	CG	180.2
40	GLU	CD	182.8
43	HIS	HD1	6.58
43	HIS	CG	135.97
44	GLU	CD	184.0
54	TYR	CZ	157.876
60	HIS	HD1	6.99
60	HIS	CG	132.02
61	ASN	CG	177.2
62	GLU	CD	183.6
63	PHE	CG	138.64
67	GLU	CD	183.4
68	GLU	CD	183.6
70	GLU	CD	183.5
72	GLU	CD	183.4
77	GLU	CD	183.8
86	GLU	CD	183.1
88	ASP	CG	180.1
89	ASN	CG	179.1
95	PHE	CG	138.19
103	GLU	CD	183.2
104	PHE	CG	139.2
105	ASN	CG	177.7
107	ASP	CG	180.6
111	ASN	CG	173.9
117	ASP	CG	180.8
120	TYR	CG	130.1
120	TYR	CZ	157.17

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	790	722	91.4
¹³C chemical shifts	586	567	96.8
¹⁵N chemical shifts	137	135	98.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	264	261	98.9
¹³C chemical shifts	254	252	99.2
¹⁵N chemical shifts	125	123	98.4

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	526	461	87.6
¹³C chemical shifts	332	315	94.9
¹⁵N chemical shifts	12	12	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	69	92.0
¹³C chemical shifts	75	69	92.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	39	84.8
¹³C chemical shifts	46	37	80.4

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_3
- Status: OK
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 37.8%
- Total number of restraints: 68
- Weight of restraints: 1.0 (68)
- Potential type of restraints: square-well-parabolic (68)
- Range of distance target values: 1.95, 2.85 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 95.3%
- Total number of restraints: 185
- Total number of restraints per polymer type: 185
- Weight of restraints: 1.0 (185)
- Potential type of restraints: square-well-parabolic (185)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords LFABP, NMR, iLBP, oleate, FABP, apo, protein

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Found 1 Document (0.695 seconds)

BMRB: 15434

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. LFABP, : 1 : 4 : 1 : 217 entities Detail

Interaction partners 1. LFABP, : 2 interactors Detail

Experiments performed 6 experiments Detail

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NMR combined restraints 4 contents Detail