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- PDB-2q2b: Crystal structure of the C-terminal domain of mouse acyl-CoA thio... -

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Open data

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Basic information

Entry

Database: PDB / ID: 2q2b

Title

Crystal structure of the C-terminal domain of mouse acyl-CoA thioesterase 7

Components

Cytosolic acyl coenzyme A thioester hydrolase

Keywords

HYDROLASE / Acot7 / C-terminal domain

Function / homology

Function and homology information

palmitoyl-CoA hydrolase / long-chain fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / fatty acid catabolic process / carboxylic ester hydrolase activity / neuron projection / mitochondrial matrix / neuronal cell body / identical protein binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Guncar, G. / Forwood, J.K. / Kobe, B.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for recruitment of tandem hotdog domains in acyl-CoA thioesterase 7 and its role in inflammation.
Authors: Forwood, J.K. / Thakur, A.S. / Guncar, G. / Marfori, M. / Mouradov, D. / Meng, W. / Robinson, J. / Huber, T. / Kellie, S. / Martin, J.L. / Hume, D.A. / Kobe, B.

History

Deposition	May 27, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.3	Aug 30, 2023	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

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	2q2b.cif.gz	70.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2q2b.ent.gz	53.6 KB	Display	PDB format
PDBx/mmJSON format	2q2b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2q2b_validation.pdf.gz	433.6 KB	Display	wwPDB validaton report
Full document	2q2b_full_validation.pdf.gz	441 KB	Display
Data in XML	2q2b_validation.xml.gz	12.9 KB	Display
Data in CIF	2q2b_validation.cif.gz	17 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q2/2q2b ftp://data.pdbj.org/pub/pdb/validation_reports/q2/2q2b	HTTPS FTP

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Related structure data

Related structure data	2v1oC 1vpmS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5k0l-d 4ad9-2 2qq2-2 5k0n-d 6vfy-d 1hmd-3 1hmd-1 4ad9-1 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	#90 - Jun 2007 Fatty Acid Synthase similarity (1)

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Assembly

Deposited unit

A: Cytosolic acyl coenzyme A thioester hydrolase

B: Cytosolic acyl coenzyme A thioester hydrolase

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

1

A: Cytosolic acyl coenzyme A thioester hydrolase

B: Cytosolic acyl coenzyme A thioester hydrolase

A: Cytosolic acyl coenzyme A thioester hydrolase

B: Cytosolic acyl coenzyme A thioester hydrolase

A: Cytosolic acyl coenzyme A thioester hydrolase

B: Cytosolic acyl coenzyme A thioester hydrolase

defined by author&software
120 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Cytosolic acyl coenzyme A thioester hydrolase

B: Cytosolic acyl coenzyme A thioester hydrolase

x 6

defined by software
239 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	4_556	y,x,-z+1	1
crystal symmetry operation	5_556	x-y,-y,-z+1	1
crystal symmetry operation	6_556	-x,-x+y,-z+1	1

Unit cell

Length a, b, c (Å)	136.743, 136.743, 99.833
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

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Components

#1: Protein

Cytosolic acyl coenzyme A thioester hydrolase / Long chain acyl-CoA thioester hydrolase / CTE-II / CTE-IIa / Brain acyl-CoA hydrolase / Acyl-CoA ...

Mass: 19956.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Acot7, Bach / Plasmid: pDEST-17 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q91V12, palmitoyl-CoA hydrolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.31 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20-30%PEG 3350, 0.1M Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 6, 2005
Radiation	Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.5→28.4 Å / Num. obs: 11896 / Redundancy: 2.3 % / R_merge(I) obs: 0.051 / Net I/σ(I): 18.3
Reflection shell	Resolution: 2.5→2.57 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1480

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
CrystalClear		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VPM

Resolution: 2.5→28.39 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.912 / SU B: 23.407 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.478 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2878	629	5 %	RANDOM
R_work	0.22209	-	-	-
obs	0.22516	11896	99.86 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 38.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.42 Å²	0.21 Å²	0 Å²
2-	-	0.42 Å²	0 Å²
3-	-	-	-0.64 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→28.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2187	0	0	55	2242

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	2185
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.375	1.955	2944
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.857	5	276
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.36	23.871	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.979	15	376
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.11	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	333
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1628
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	954
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	1472
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	117
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.165	0.2	26
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.169	0.2	3
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.377	1.5	1425
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.635	2	2241
X-RAY DIFFRACTION	r_scbond_it	1.02	3	837
X-RAY DIFFRACTION	r_scangle_it	1.662	4.5	703
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.382	50	-
R_work	0.3	864	-
obs	-	-	99.78 %

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	18.356	-1.3834	-10.8359	5.447	-0.539	12.1568	0.8709	-0.2142	1.0669	0.4999	-0.0288	0.672	-2.1788	0.1851	-0.8421	0.5414	-0.0192	0.0513	0.1449	0.0441	0.2871	-25.8886	11.9085	36.2347
2	7.1383	8.5659	-1.6004	14.4028	-1.804	0.3621	-0.2233	0.9732	-0.9825	-1.7342	0.3933	-1.4261	0.2258	0.5009	-0.17	0.6346	-0.0264	-0.0127	0.6809	-0.0225	0.3131	-11.7239	2.3034	15.3564
3	4.4642	-2.6756	-6.6613	9.0858	5.6258	21.5116	0.3495	0.2329	-0.2099	0.1521	-0.0901	-0.2644	-0.1201	0.4525	-0.2594	0.0656	-0.1083	-0.0844	0.1551	0.0327	0.0471	-17.2982	1.7215	29.0577
4	1.8278	-0.493	-1.4371	5.3435	-0.7172	6.4602	-0.0132	0.1669	-0.0258	0.3248	-0.347	0.5267	-0.4263	0.1926	0.3602	0.09	0.0152	-0.0596	0.2225	0.0471	0.1856	-22.2966	-1.1124	33.8381
5	8.6015	3.4082	-12.1961	14.9082	-3.307	17.4645	0.3717	1.7465	1.3636	-2.6091	0.3043	0.7175	-0.0419	0.2784	-0.676	0.7448	0.0446	-0.0009	0.6915	0.04	0.3238	-17.176	2.605	11.0584
6	11.068	4.8211	-7.7397	7.5875	-4.7876	6.5782	-0.0039	0.7469	0.2586	0.0141	0.1848	0.5513	-0.4708	-0.5097	-0.1809	0.109	0.0601	-0.1248	0.2231	0.0213	0.1134	-25.1163	5.4054	28.2902
7	4.4787	0.3412	-2.4069	3.1804	-0.8791	13.5116	0.1796	0.3868	0.1262	0.1124	0.514	0.7873	-0.6168	-0.706	-0.6936	-0.0012	-0.0049	-0.07	0.0688	0.0351	0.1799	-26.603	1.5006	30.9864
8	29.9888	-4.6262	4.7762	0.7149	-0.7935	3.3167	0.1423	0.1261	2.6353	-1.8805	-0.3955	0.1865	-1.2846	0.44	0.2532	1.033	-0.0758	-0.116	0.6285	-0.0114	0.5313	-19.3887	12.8629	11.0703
9	3.7736	-0.758	2.9113	3.2629	-3.3025	32.3039	0.2359	-0.0471	-0.1508	-0.0838	0.2846	0.4162	1.2109	0.7399	-0.5205	0.0589	-0.0081	-0.0931	0.0071	-0.0134	0.1505	-22.7089	-3.4874	35.8235
10	22.3448	-13.4422	6.2107	19.041	-7.8184	7.6873	0.4093	0.1154	0.3572	0.8324	-0.1491	0.658	-0.8037	-0.3051	-0.2603	0.2859	0.0478	0.1318	0.1506	0.0694	0.2064	-30.0056	1.9453	43.8228
11	13.4536	-1.0246	6.8752	17.3993	-3.1224	13.0081	-0.0328	0.2359	1.2447	-0.5193	-0.2849	1.0525	-1.4062	-1.8532	0.3178	0.3333	0.248	0.0563	0.4319	0.1487	0.5907	-38.859	7.5782	32.6668
12	0.7869	2.2448	-3.962	39.8151	-7.9245	25.2336	0.1171	0.6759	-0.5384	-0.1076	0.63	0.4323	0.3478	-1.9923	-0.7471	-0.0498	-0.1673	-0.123	0.4354	0.0769	0.6078	-36.1088	-6.4238	33.4794
13	6.3556	-1.5677	2.2013	9.9395	3.5912	9.6953	0.4081	1.2862	-1.4422	-0.8029	-0.5709	0.5056	1.7235	0.3419	0.1628	0.4829	0.1541	-0.0854	0.5104	-0.3127	0.3959	-13.4715	-25.8141	13.9632
14	17.5245	-11.115	-4.0913	21.6928	5.1719	1.4087	0.2178	-0.3892	2.5968	0.5356	0.0899	-1.5275	-0.8825	-0.4445	-0.3078	0.3686	0.0223	-0.0881	0.4917	-0.1414	0.3453	-5.5464	-10.657	33.8868
15	6.6162	-5.9767	-7.7356	7.6892	2.2215	18.9639	-0.0388	-0.3927	0.0959	0.1158	0.25	-0.1199	-1.1239	0.9312	-0.2111	0.0911	-0.0381	-0.0853	0.2837	-0.0271	0.1048	-12.7685	-7.6994	27.5797
16	12.311	-2.3785	-5.929	5.352	-0.9207	26.1296	-0.1527	1.1355	-0.3003	-0.5882	0.1827	0.5477	-0.0711	1.9445	-0.03	0.2726	0.0845	-0.1628	0.4199	-0.1218	0.1022	-12.7512	-14.711	16.6395
17	3.5788	-2.3464	0.3257	6.0246	4.3564	6.8249	0.5258	1.0309	-0.4877	-1.2108	-0.4718	0.1598	-0.3911	0.3454	-0.054	0.3651	0.0215	-0.1399	0.4597	-0.0867	0.3159	-18.5106	-13.2354	16.2696
18	19.824	1.5971	-7.2775	11.8381	-7.1277	6.3259	-0.2979	-2.6633	-0.3029	1.8463	0.4044	0.2644	-1.2101	-0.0252	-0.1066	0.4107	0.0656	-0.0259	0.5937	-0.2291	0.329	-10.7311	-13.3062	38.2338
19	10.247	0.3091	1.5939	3.3783	-1.7593	2.2567	0.5775	0.8048	-0.8622	-0.9598	-0.3527	0.4688	1.0509	-0.2801	-0.2248	0.4411	0.0398	-0.1812	0.3167	-0.2282	0.2951	-20.2083	-19.4219	16.9919
20	20.1045	-1.7567	26.9923	4.4169	-3.5974	53.6764	0.8416	0.348	-0.9637	-0.4259	-0.3927	0.4597	1.3777	0.1958	-0.4489	0.0246	0.0417	-0.0849	0.0936	-0.1811	0.2517	-16.8109	-18.8548	25.0038
21	23.9123	-3.7213	5.5954	6.1957	-8.7867	13.4349	0.0462	-2.3707	-0.9699	0.4424	-0.1212	-0.2812	0.4943	0.4079	0.0749	0.3228	0.05	-0.0497	0.4712	0.0135	0.2701	-11.0026	-19.4513	37.1563
22	3.2883	-0.2599	0.571	3.6677	1.4885	5.926	0.1674	1.267	0.4306	-1.564	-0.0073	-0.3378	-0.516	0.5406	-0.1601	0.6229	0.0714	-0.0884	0.6794	-0.0524	0.3743	-19.9853	-10.608	9.6988
23	9.6552	0.0657	-2.9328	13.7769	-0.0978	8.2277	0.3486	1.1463	-1.4391	-0.5733	-0.8758	0.5725	0.3884	-0.1929	0.5272	0.4617	-0.0669	-0.3174	0.5154	-0.3117	0.639	-23.7341	-25.3676	12.5324
24	14.1319	6.1782	-8.8203	25.4768	-0.5029	20.7728	0.4259	0.5165	-1.8395	1.4393	-0.3143	3.4167	-0.0098	-0.7183	-0.1116	0.2886	-0.1429	-0.3941	0.768	-0.2752	0.5788	-32.1102	-18.9776	17.5968

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	177 - 188	18 - 29
2	X-RAY DIFFRACTION	2	A	A	189 - 206	30 - 47
3	X-RAY DIFFRACTION	3	A	A	207 - 221	48 - 62
4	X-RAY DIFFRACTION	4	A	A	222 - 238	63 - 79
5	X-RAY DIFFRACTION	5	A	A	239 - 245	80 - 86
6	X-RAY DIFFRACTION	6	A	A	246 - 258	87 - 99
7	X-RAY DIFFRACTION	7	A	A	259 - 270	100 - 111
8	X-RAY DIFFRACTION	8	A	A	271 - 281	112 - 122
9	X-RAY DIFFRACTION	9	A	A	282 - 298	123 - 139
10	X-RAY DIFFRACTION	10	A	A	299 - 307	140 - 148
11	X-RAY DIFFRACTION	11	A	A	308 - 317	149 - 158
12	X-RAY DIFFRACTION	12	A	A	318 - 326	159 - 167
13	X-RAY DIFFRACTION	13	B	B	177 - 188	18 - 29
14	X-RAY DIFFRACTION	14	B	B	189 - 203	30 - 44
15	X-RAY DIFFRACTION	15	B	B	204 - 212	45 - 53
16	X-RAY DIFFRACTION	16	B	B	213 - 221	54 - 62
17	X-RAY DIFFRACTION	17	B	B	222 - 238	63 - 79
18	X-RAY DIFFRACTION	18	B	B	239 - 247	80 - 88
19	X-RAY DIFFRACTION	19	B	B	248 - 261	89 - 102
20	X-RAY DIFFRACTION	20	B	B	262 - 271	103 - 112
21	X-RAY DIFFRACTION	21	B	B	272 - 286	113 - 127
22	X-RAY DIFFRACTION	22	B	B	287 - 297	128 - 138
23	X-RAY DIFFRACTION	23	B	B	298 - 315	139 - 156
24	X-RAY DIFFRACTION	24	B	B	316 - 326	157 - 167

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