PDB-7o0k: Crystal structure of recombinant chichen liver Bile Acid Binding ...

ID or keywords:

Entry

Database: PDB / ID: 7o0k

Title

Crystal structure of recombinant chichen liver Bile Acid Binding Protein (cL-BABP) in complex with cholic acid

Components

Fatty acid-binding protein, liver

Keywords

LIPID BINDING PROTEIN / fatty acid binding protein / chicken liver bile acid binding protein / recombinant / bile acid / cholic acid

Function / homology

Function and homology information

fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.83 Å

Authors

Tassone, G. / Pozzi, C.

Citation

Journal: Biomolecules / Year: 2021
Title: Validation of Recombinant Chicken Liver Bile Acid Binding Protein as a Tool for Cholic Acid Hosting.
Authors: Tassone, G. / Orlandini, M. / Olivucci, M. / Pozzi, C.

History

Deposition	Mar 26, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 12, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7o0k.cif.gz	119.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7o0k.ent.gz	93.9 KB	Display	PDB format
PDBx/mmJSON format	7o0k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7o0k_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	7o0k_full_validation.pdf.gz	1.4 MB	Display
Data in XML	7o0k_validation.xml.gz	13.2 KB	Display
Data in CIF	7o0k_validation.cif.gz	17.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o0/7o0k ftp://data.pdbj.org/pub/pdb/validation_reports/o0/7o0k	HTTPS FTP

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Related structure data

Related structure data	7o0jC 1tvqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5l8i-2 6xvy-1 3fr4-d 4a1y-3 2qo6-d 4q26-4 1fdq-1 1slt-3 1fdq-2 2jn3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (2) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Fatty acid-binding protein, liver

B: Fatty acid-binding protein, liver

hetero molecules

30.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fatty acid-binding protein, liver

hetero molecules

defined by author&software
Evidence: gel filtration
15.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fatty acid-binding protein, liver

hetero molecules

defined by author&software
15.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.679, 62.920, 77.569
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver basic FABP / LB-FABP / Liver bile acid-binding protein / L- ...Fatty acid-binding protein 1 / Liver basic FABP / LB-FABP / Liver bile acid-binding protein / L-BABP / Liver-type fatty acid-binding protein / L-FABP Mass: 14513.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: FABP1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3)GOLD / References: UniProt: P80226
#2: Chemical	ChemComp-CHD / CHOLIC ACID Mass: 408.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₄H₄₀O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.93 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 % vol/vol 2-propanol, 20 % PEG4000 and 100 mM Hepes, pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 24, 2020
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.83→62.92 Å / Num. obs: 26839 / % possible obs: 99.8 % / Redundancy: 7.4 % / B_iso Wilson estimate: 32.2 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.061 / R_pim(I) all: 0.025 / R_rim(I) all: 0.066 / Net I/σ(I): 13.6
Reflection shell	Resolution: 1.83→1.93 Å / R_merge(I) obs: 0.856 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3830 / CC_1/2: 0.819 / R_pim(I) all: 0.331 / R_rim(I) all: 0.919

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TVQ

1tvq

Resolution: 1.83→48.87 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.935 / SU B: 9.331 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2803	1326	5 %	RANDOM
R_work	0.2343	-	-	-
obs	0.2366	25436	99.66 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 127.46 Å² / B_iso mean: 45.493 Å² / B_iso min: 23.7 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.49 Å²	0 Å²	-0 Å²
2-	-	-0.65 Å²	0 Å²
3-	-	-	0.16 Å²

Refine analyze

Luzzati coordinate error free: 0.3292 Å

Refinement step

Cycle: final / Resolution: 1.83→48.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1921	0	116	112	2149
B_iso mean	-	-	33.79	46.85	-
Num. residues	-	-	-	-	251

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	2077
X-RAY DIFFRACTION	r_angle_refined_deg	2.041	1.643	2844
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.211	5	249
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.818	23.333	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.4	15	340
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.632	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	319
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	1476

LS refinement shell

Resolution: 1.83→1.877 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.356	86	-
R_work	0.346	1834	-
all	-	1920	-
obs	-	-	99.17 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.4407	-2.9292	3.9771	2.6408	-0.86	5.6911	0.0982	-0.328	0.3415	-0.4266	-0.1057	-0.5927	-0.3948	-0.675	0.0075	0.187	0.0823	0.0925	0.1458	0.0665	0.2875	13.962	-6.263	-7.775
2	17.9742	1.4454	-8.7172	8.9647	-3.482	19.0798	-0.1386	1.444	0.4185	-0.516	-0.0418	0.4741	0.2965	-0.0026	0.1804	0.3561	0.0249	-0.0871	0.289	-0.0301	0.1039	12.129	-19.214	-19.009
3	6.4239	-4.236	-1.0481	15.844	3.6823	0.8571	0.155	0.1167	-0.7611	1.0469	-0.1605	-0.0341	0.2518	-0.0434	0.0055	0.5203	-0.0538	0.0686	0.3664	-0.0481	0.2522	6.656	-26.767	-16.092
4	8.2403	-3.5066	6.7782	4.8714	-2.262	25.969	0.2488	0.467	-0.7659	-0.5806	-0.2394	0.8305	-0.0684	-1.5458	-0.0094	0.2267	-0.1068	-0.1284	0.6224	-0.0651	0.1662	1.205	-19.812	-17.857
5	9.8063	1.6069	8.454	1.9079	1.5115	9.8815	-0.1929	-0.2169	0.5909	-0.2818	0.2887	-0.2972	-0.2996	-0.4248	-0.0958	0.1075	0.0372	0.0463	0.2753	-0.0601	0.2705	9.577	-8.881	-4.799
6	8.2258	-2.9821	2.1917	1.391	-0.3179	7.3828	-0.58	-0.439	0.5483	0.0732	0.1841	-0.2943	-0.9755	-0.0127	0.3959	0.1635	0.0152	-0.0286	0.3777	-0.033	0.1671	14.273	-12.194	4.89
7	21.9284	0.5182	-4.4834	0.4563	-2.4262	13.0435	-0.2978	0.1704	-0.663	0.0574	0.0932	-0.0321	-0.2663	-0.4659	0.2046	0.062	0.0669	-0.0521	0.4256	0.0055	0.2249	-0.132	-12.797	-5.789
8	5.6458	-0.0306	1.4293	1.8599	0.6257	3.0597	-0.2714	-0.6804	-0.3373	-0.1301	0.0306	0.0275	0.0113	-0.5127	0.2408	0.0396	-0.0039	0.0506	0.337	0.0461	0.136	11.035	-21.284	2.114
9	11.459	5.6871	-2.4905	3.529	-0.9063	4.083	-0.0927	-0.6316	-0.0599	-0.1013	-0.2715	-0.317	0.2457	0.2103	0.3642	0.0452	0.047	0.0379	0.28	0.0683	0.2853	23.492	-18.507	0.791
10	1.767	-1.6199	1.0571	7.0767	-2.0354	1.9036	0.0048	-0.2778	0.1207	-0.4908	-0.3832	-0.4164	0.2673	0.2381	0.3784	0.1003	0.0673	0.1083	0.2261	0.0301	0.2522	21.195	-18.629	-5.613
11	2.4736	1.8744	0.7107	20.6297	1.3707	2.4221	0.014	0.2173	0.2497	-0.5168	-0.3087	-0.1841	-0.0461	-0.0132	0.2947	0.2091	0.0774	0.0768	0.1954	0.0395	0.2093	18.608	-13.533	-10.351
12	2.6748	-1.2822	-2.6229	9.9032	2.2837	4.6683	-0.2159	0.2745	0.2749	0.0064	0.0305	0.0094	0.1877	0.1208	0.1855	0.2266	0.0531	0.0205	0.219	0.0662	0.1864	16.212	-11.556	-12.523
13	11.4279	-12.283	5.2787	13.3454	-5.6644	2.4403	0.8637	0.5433	-0.1491	-0.5885	-0.8195	0.0613	0.4264	0.2469	-0.0442	0.8916	-0.4727	-0.1227	0.5074	0.4104	0.7647	34.726	-24.833	-32.291
14	0.7677	0.2427	-1.3181	11.9643	0.6247	6.3046	0.294	-0.5574	0.2579	0.4535	-0.3372	-0.0872	0.4192	0.0923	0.0432	0.3574	-0.3504	0.1825	0.6753	-0.243	0.2041	30.795	-9.349	-22.613
15	14.0772	9.8008	0.3549	6.8642	0.238	0.1382	0.1851	-0.0941	1.5787	0.1942	-0.1416	1.0844	-0.2696	-0.1219	-0.0435	0.6431	0.1838	0.1557	0.4171	0.0264	0.2944	22.927	-0.239	-27.892
16	7.7493	-8.7847	-5.8842	23.6058	-3.6885	12.3581	0.1992	0.2704	0.0574	0.0252	0.3578	0.6425	-0.2499	-0.6945	-0.557	0.3728	-0.0852	0.1067	0.5038	-0.0364	0.112	20.562	-8.474	-22.689
17	8.7142	-8.0338	-3.931	8.6772	3.2292	1.9964	0.1256	0.5186	-0.4363	-0.1163	-0.3777	-0.1055	0.1574	-0.4405	0.2521	0.5989	-0.3247	-0.1783	0.3568	0.1239	0.3419	29.328	-22.314	-34.387
18	13.1309	-2.2129	-5.6651	2.2972	1.5996	2.9948	-0.2499	0.6573	-0.0973	0.4153	0.1245	-0.151	0.689	-0.5001	0.1254	0.7073	-0.3727	0.089	0.3188	-0.1138	0.2659	26.127	-18.478	-37.528
19	2.9788	-0.6768	-0.8981	2.5645	-0.3504	2.6403	0.1953	0.3361	-0.0983	-0.2315	-0.2013	-0.1178	0.0784	-0.3393	0.006	0.1442	0.0703	-0.0206	0.2133	-0.0215	0.1084	32.524	-11.775	-43.584
20	5.4314	-0.5388	-3.1264	3.1552	-1.2789	2.6159	-0.087	-0.2192	0.0718	0.186	0.1699	0.0264	-0.0562	0.0548	-0.0829	0.2197	0.0152	-0.0316	0.1115	-0.0504	0.2603	41.573	-9.262	-37.347
21	5.0641	-1.9054	0.51	16.4664	-4.0712	2.3331	0.1586	-0.4732	-0.2299	0.4395	-0.1375	-0.7572	0.1984	0.281	-0.0211	0.257	0.0074	-0.0461	0.1687	0.0246	0.2427	40.098	-13.545	-32.434
22	30.0108	20.3541	-3.3255	13.8059	-2.2562	0.3691	0.5333	-0.9547	-1.1348	0.328	-0.6578	-0.7694	-0.0362	0.1119	0.1244	0.95	0.1994	-0.123	0.2409	0.2308	0.3508	38.794	-22.825	-26.935
23	1.2888	-0.0101	-1.1152	0.0023	0.0656	3.9053	0.1712	-0.5119	0.0477	-0.0126	-0.0093	-0.0009	0.0324	0.0893	-0.162	0.237	-0.0499	-0.0539	0.2552	-0.0047	0.1586	36.125	-7.318	-27.922
24	16.974	1.9062	-2.673	5.3262	-3.617	2.5756	0.192	0.1935	-0.8421	0.2805	-0.3329	-0.0923	-0.1693	0.2177	0.1409	1.0254	-0.11	-0.1848	0.2642	0.1669	0.1852	33.183	-23.693	-25.45

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 12
2	X-RAY DIFFRACTION	2	A	13 - 19
3	X-RAY DIFFRACTION	3	A	20 - 26
4	X-RAY DIFFRACTION	4	A	27 - 33
5	X-RAY DIFFRACTION	5	A	34 - 44
6	X-RAY DIFFRACTION	6	A	45 - 52
7	X-RAY DIFFRACTION	7	A	53 - 58
8	X-RAY DIFFRACTION	8	A	59 - 79
9	X-RAY DIFFRACTION	9	A	80 - 89
10	X-RAY DIFFRACTION	10	A	90 - 105
11	X-RAY DIFFRACTION	11	A	106 - 114
12	X-RAY DIFFRACTION	12	A	115 - 126
13	X-RAY DIFFRACTION	13	B	1 - 8
14	X-RAY DIFFRACTION	14	B	9 - 19
15	X-RAY DIFFRACTION	15	B	20 - 29
16	X-RAY DIFFRACTION	16	B	30 - 35
17	X-RAY DIFFRACTION	17	B	36 - 44
18	X-RAY DIFFRACTION	18	B	45 - 59
19	X-RAY DIFFRACTION	19	B	60 - 85
20	X-RAY DIFFRACTION	20	B	86 - 97
21	X-RAY DIFFRACTION	21	B	98 - 102
22	X-RAY DIFFRACTION	22	B	103 - 109
23	X-RAY DIFFRACTION	23	B	110 - 121
24	X-RAY DIFFRACTION	24	B	122 - 126

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