PDB-7fza: Crystal Structure of apo human FABP4, cubic form

ID or keywords:

Entry

Database: PDB / ID: 7fza

Title

Crystal Structure of apo human FABP4, cubic form

Components

Fatty acid-binding protein, adipocyte

Keywords

LIPID BINDING PROTEIN /

FATTY ACID BINDING PROTEIN /

CYTOPLASM / LIPID-BINDING / TRANSPORT /

PROTEIN BINDING

Function / homology

Function and homology information

hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion /

long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation /

lipid droplet ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.601 Å

Authors

Ehler, A. / Benz, J. / Obst, U. / Rudolph, M.G.

Funding support

Switzerland, 1items

Citation

Journal: To be published
Title: Crystal Structure of apo human FABP4
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.

History

Deposition	Apr 27, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 14, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7fza.cif.gz	121.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7fza.ent.gz	96.5 KB	Display	PDB format
PDBx/mmJSON format	7fza.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fz/7fza ftp://data.pdbj.org/pub/pdb/validation_reports/fz/7fza	HTTPS FTP

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Group deposition

ID	G_1002264 (222 entries) 7fvu 7fvv 7fvw 7fvx 7fvy 7fvz 7fw0 7fw1 7fw2 7fw3
Title	To be published
Type	undefined
Description	A set of fabp crystal structures

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Related structure data

Similar structure data	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 (3) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Fatty acid-binding protein, adipocyte

B: Fatty acid-binding protein, adipocyte

hetero molecules

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

1

A: Fatty acid-binding protein, adipocyte

hetero molecules

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

2

B: Fatty acid-binding protein, adipocyte

hetero molecules

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

Unit cell

Length a, b, c (Å)	137.105, 137.105, 137.105
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	207
Space group name H-M	P432

#1: Protein	Fatty acid-binding protein, adipocyte / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP / Fatty acid-binding protein 4 Mass: 15022.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.57 Å³/Da / Density % sol: 65.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.6→45.7 Å / Num. obs: 14121 / % possible obs: 99.8 % / Redundancy: 32.78 % / B_iso Wilson estimate: 75.17 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.126 / R_rim(I) all: 0.155 / R_sym value: 0.126 / Χ²: 0.811 / Net I/σ(I): 22.88 / Num. measured all: 471794 / Scaling rejects: 38

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.6-2.67	34.925	4.33	1.16	35624	1018	1020	0.429	4.394	100
2.67-2.74	34.525	3.195	1.63	34387	996	996	0.671	3.242	100
2.74-2.82	33.248	2.573	2.03	31619	951	951	0.717	2.612	100
2.82-2.91	33.784	1.834	2.91	31554	934	934	0.853	1.862	100
2.91-3	34.567	1.507	3.58	31802	920	920	0.912	1.529	100
3-3.11	35.362	0.897	6.15	31366	887	887	0.955	0.91	100
3.11-3.23	34.793	0.581	9.39	29574	851	850	0.985	0.59	99.9
3.23-3.36	33.984	0.366	14.23	28037	825	825	0.99	0.371	100
3.36-3.51	32.481	0.244	21.22	25822	795	795	0.995	0.248	100
3.51-3.68	33.163	0.187	25.94	24872	748	750	0.998	0.19	100
3.68-3.88	34.55	0.15	31.5	25394	737	735	0.998	0.152	99.7
3.88-4.11	34.093	0.117	37.28	23456	688	688	0.999	0.119	100
4.11-4.4	33.232	0.079	49.91	21800	656	656	1	0.08	100
4.4-4.75	31.375	0.063	59.75	19390	618	618	0.999	0.064	100
4.75-5.2	33.333	0.064	58.3	18833	565	565	1	0.065	100
5.2-5.82	33.023	0.064	58.72	17370	526	526	0.999	0.065	100
5.82-6.72	30.487	0.061	59.87	14329	470	470	0.999	0.062	100
6.72-8.23	30.362	0.049	67.94	12327	406	406	1	0.05	100
8.23-11.63	28.675	0.032	87.75	9434	330	329	1	0.033	99.7
11.63-48.474	22.768	0.031	82.44	4804	217	211	0.998	0.032	97.2

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	dev_707	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.601→48.474 Å / FOM work R set: 0.7516 / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.59 / Stereochemistry target values: ML / Details: failed attempt to co-crystallize RO1120653

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2511	668	4.74 %	RANDOM
R_work	0.1981	13439	-	-
obs	0.2007	14107	99.8 %	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 64.575 Å² / k_sol: 0.363 e/Å³

Displacement parameters

B_iso max: 171.06 Å² / B_iso mean: 79.44 Å² / B_iso min: 33.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	-0 Å²

Refinement step

Cycle: final / Resolution: 2.601→48.474 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2100	0	32	13	2145
B_iso mean	-	-	119.28	65.08	-
Num. residues	-	-	-	-	270

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2153
X-RAY DIFFRACTION	f_angle_d	1.166	2896
X-RAY DIFFRACTION	f_chiral_restr	0.075	332
X-RAY DIFFRACTION	f_plane_restr	0.003	360
X-RAY DIFFRACTION	f_dihedral_angle_d	16.744	790

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 5

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.6013-2.8021	0.4711	126	0.4065	2605	2731	100
2.8021-3.0841	0.374	123	0.312	2638	2761	100
3.0841-3.5302	0.3011	121	0.2318	2665	2786	100
3.5302-4.4472	0.2372	158	0.1717	2644	2802	99
4.4472-48.4823	0.1989	140	0.1616	2887	3027	100

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	4.0702	-0.3577	-2.3283	1.5445	1.2607	8.4143	-0.1033	-0.7746	0.1406	-0.0947	0.0189	0.0633	-0.2898	0.5805	0.077	0.4047	0.001	0.0276	0.3984	-0.0167	0.7221	-21.6531	59.7901	14.3496
2	2.0318	0.7675	-0.1757	1.8814	-0.2645	3.3973	0.0118	0.5051	-0.2693	-0.4697	0.0418	0.006	0.302	0.0986	-0.1804	0.6037	-0.0352	0.0111	0.3981	0.0022	0.431	-18.6085	52.8866	-1.2927
3	3.3118	-0.6354	-3.4539	7.5592	0.8909	3.5895	-0.103	0.0897	0.6325	-0.7384	0.0738	1.0307	-0.6583	-0.5989	0.2332	0.3739	-0.0144	-0.0866	0.4355	0.0099	0.6392	-31.9037	58.7803	9.1438
4	4.668	0.6778	-0.7427	6.0547	-1.0155	6.5036	0.0734	0.4972	0.0322	-0.6679	-0.0638	-0.4929	-0.8264	0.3693	-0.5523	0.6211	-0.0649	-0.186	0.5527	-0.0377	0.9218	-28.2368	58.0265	0.1988
5	3.3068	0.5243	-1.1736	4.0308	-0.9623	3.6774	0.0266	0.2548	-0.6807	-0.071	0.096	0.9296	1.2553	-0.3661	-0.166	0.5462	-0.0108	-0.0716	0.3355	0.0155	0.712	-28.0069	46.7509	7.6192
6	3.5679	-1.1194	-0.9373	6.59	3.2576	4.5147	-0.3289	-0.2584	-0.0001	-0.4676	0.4726	-0.0877	0.54	0.6078	-0.0991	0.6135	0.0203	-0.0004	0.36	-0.0055	0.5104	-16.0507	53.2359	9.5089
7	5.7069	2.2459	-3.5871	3.4705	-3.0016	3.2327	0.2818	1.7607	-0.8676	-0.4768	0.0548	0.3193	0.0818	-0.3976	-0.3507	0.4513	0.0501	-0.1185	0.5589	0.0205	0.8152	-34.0028	70.3022	-23.2629
8	2.3183	-0.2259	-0.4771	2.8121	-0.532	0.425	-0.6652	0.2469	-0.6575	0.1278	0.654	1.0736	0.7864	-0.9886	0.0096	0.7491	-0.261	0.1555	0.8712	-0.0063	1.2248	-50.3173	54.9035	-11.3353
9	5.5032	0.27	0.5459	3.6564	-1.1925	3.3748	-0.0311	-0.72	-0.143	0.6201	0.4101	0.3752	0.0522	0.2768	-0.2724	0.4355	0.014	0.0414	0.4779	-0.0157	0.6728	-35.5827	64.7173	-12.0768
10	6.8562	-0.5708	-5.3641	1.4545	0.9309	6.8353	0.4681	-1.5363	-0.2994	0.654	-0.7831	1.413	-0.5379	-0.0121	0.3888	0.5976	-0.1872	0.067	0.9053	0.0252	0.9631	-37.4751	58.8057	-6.8419
11	2.193	1.3631	-1.1164	3.8693	-0.7514	2.6382	-0.245	0.1584	-0.4198	-0.7819	0.4778	0.1869	1.0887	-0.4403	-0.3086	0.76	-0.1487	-0.1911	0.5273	-0.0859	0.7152	-33.9413	52.2215	-17.8054
12	1.8453	0.1029	-1.5534	7.1697	2.4284	2.2	0.4163	0.232	-0.0176	-0.0075	-0.4862	1.2901	0.5813	-0.5382	0.1833	0.6063	-0.2335	-0.2827	0.7828	-0.024	1.0119	-41.4765	54.72	-21.7077
13	2.4446	1.3239	0.1804	5.8311	-0.4453	2.3148	-0.3923	0.6864	0.2972	-0.8319	0.2989	1.5358	0.3121	-0.6141	-0.1368	0.4723	-0.2076	-0.0621	0.6242	-0.0792	1.0751	-47.3121	61.1349	-19.6921

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq -3:14)	A	-3 - 14
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 15:45)	A	15 - 45
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 46:54)	A	46 - 54
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 55:64)	A	55 - 64
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 65:109)	A	65 - 109
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 110:131)	A	110 - 131
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq -3:5)	B	-3 - 5
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 6:35)	B	6 - 35
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 36:54)	B	36 - 54
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 55:64)	B	55 - 64
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 65:97)	B	65 - 97
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 98:109)	B	98 - 109
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 110:131)	B	110 - 131

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