PDB-4p13: Medium chain acyl-CoA dehydrogenase, K304E mutant

ID or keywords:

Entry

Database: PDB / ID: 4p13

Title

Medium chain acyl-CoA dehydrogenase, K304E mutant

Components

Medium-chain specific acyl-CoA dehydrogenase, mitochondrial

Keywords

OXIDOREDUCTASE /

tetramer /

dehydrogenase /

oxidase

Function / homology

Function and homology information

medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked /

medium-chain acyl-CoA dehydrogenase / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / medium-chain fatty acyl-CoA dehydrogenase activity / carnitine biosynthetic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / medium-chain fatty acid metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.73 Å

Authors

Battaile, K.P. / Mohsen, A.-W. / Vockley, J.

Citation

Journal: To Be Published
Title: Medium chain acyl-CoA dehydrogenase, K304E mutant
Authors: Battaile, K.P. / Mohsen, A.-W. / Vockley, J.

History

Deposition	Feb 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

Remark 0

: statistics at the very beginning when nothing is done yet

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4p13.cif.gz	606.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4p13.ent.gz	502.7 KB	Display	PDB format
PDBx/mmJSON format	4p13.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/p1/4p13 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/4p13	HTTPS FTP

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Related structure data

Similar structure data	1ege-d 1egc-d 3mdd-1 3mpj-1 3mpj-2 3mpi-2 1egd-d 4l1f-1 1ukw-2 2vig-2 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

Deposited unit

A: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial

B: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial

C: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial

D: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial

hetero molecules

174 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	95.270, 102.590, 149.650
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Medium-chain specific acyl-CoA dehydrogenase, mitochondrial / MCAD Mass: 42655.594 Da / Num. of mol.: 4 / Mutation: K333E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACADM / Production host: Escherichia coli (E. coli) References: UniProt: P11310, medium-chain acyl-CoA dehydrogenase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.14 Å³/Da / Density % sol: 42.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG4000, 140mm Tris-acetate pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.72→32.66 Å / Num. obs: 152953 / % possible obs: 100 % / Redundancy: 6.6 % / B_iso Wilson estimate: 23.69 Å² / Net I/σ(I): 19

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Processing

Software

Name: BUSTER / Version: 2.10.0 / Classification: refinement

Refinement

Resolution: 1.73→32.66 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.96 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU R_free Blow DPI: 0.083 / SU R_free Cruickshank DPI: 0.082

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.163	7674	5.02 %	RANDOM
R_work	0.145	-	-	-
obs	0.146	152953	100 %	-

Displacement parameters

B_iso mean: 25.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.5581 Å²	0 Å²	0 Å²
2-	-	-0.5753 Å²	0 Å²
3-	-	-	-1.9828 Å²

Refine analyze

Luzzati coordinate error obs: 0.151 Å

Refinement step

Cycle: LAST / Resolution: 1.73→32.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11954	0	236	822	13012

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	12564	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.99	16995	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		4472	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		332	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1976	HARMONIC	5
X-RAY DIFFRACTION	t_it		12564	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.32
X-RAY DIFFRACTION	t_other_torsion	15.99
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1633	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies		19	HARMONIC	1
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		15889	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.73→1.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2083	550	4.91 %
R_work	0.1899	10644	-
all	0.1908	11194	-
obs	-	-	99.98 %

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	2.0495	-0.9061	1.9039	0.2876	-0.1958	1.168	0.0645	0.2796	0.0431	-0.1056	-0.0228	-0.0555	0.1047	0.116	-0.0417	-0.0275	-0.0048	0.0279	0.0463	-0.0089	0.0171	-14.8441	-5.8565	-10.3066
2	0.1068	0.5481	0.1584	1.0991	-0.5261	3.0989	0.059	-0.1192	-0.1829	0.1117	-0.0274	-0.1904	0.0504	0.1586	-0.0316	-0.0632	0.02	-0.0137	-0.0572	-0.0097	0.0589	-7.7324	-8.7794	10.7526
3	0.4854	0.0863	0.0421	0.1349	0.1156	0.3578	-0.0288	0.1197	-0.0167	-0.0589	0.0212	-0.0346	-0.0755	0.0725	0.0077	-0.0266	-0.0188	-0.0106	-0.0163	0.0051	0.0064	-10.6067	7.0783	3.491
4	0.9629	0.4737	-0.0791	0.9892	0.0551	0.6429	0.0416	0.022	0.1698	0.0168	-0.0579	0.0575	-0.159	0.0144	0.0162	-0.0151	-0.0072	-0.0307	-0.0595	0.0033	0.0123	-13.8225	17.3708	17.3913
5	0.7469	1.4406	-0.0874	4.4842	0.0088	0.2158	-0.0332	0.0101	0.0787	-0.0646	-0.0196	0.0555	-0.0517	0.0534	0.0528	-0.0238	0.0019	-0.0152	-0.0236	-0.0027	0.0062	-23.3143	-1.1409	2.8015
6	0.733	0.8841	-0.5965	2.5271	-1.3158	1.3028	-0.1365	0.1103	0.0401	-0.2008	0.1437	0.0232	0.0963	-0.0811	-0.0072	-0.048	0.0034	-0.0114	-0.017	-0.0114	-0.0395	-31.3282	-10.8205	-2.9573
7	0.4062	-0.5087	0.1373	1.5457	-0.9262	0.7383	0.0225	0.0103	-0.0067	-0.0147	-0.0937	-0.0392	0.0083	0.0923	0.0711	0.0053	-0.0013	-0.0131	-0.0061	-0.0128	0.0041	-31.2858	-6.6803	5.4677
8	0.8792	-0.8418	0.4409	2.3352	-0.8792	0.5169	-0.0428	0.0056	0.0301	0.0326	0.0047	-0.0195	-0.0431	0.0298	0.0381	-0.0107	-0.0016	-0.0126	-0.0159	-0.0106	0.0066	-30.5649	2.1385	7.1695
9	1.1266	-0.3853	0.8478	0.4736	-0.0574	1.5416	-0.035	-0.2134	0.0808	0.0438	0.0328	0.0501	-0.0001	-0.1718	0.0022	0.029	0.0268	-0.0109	-0.0046	-0.0059	-0.0647	-52.5693	-11.3258	37.9243
10	1.9011	-0.1527	-0.3506	1.8292	-0.0456	0.0243	-0.0371	-0.1469	0.0813	0.1882	-0.0676	-0.2342	-0.0299	0.1251	0.1047	0.0336	0.0104	-0.0584	0.0036	-0.0039	-0.0322	-30.5032	-15.4495	38.729
11	0.2832	-0.1969	0.0185	0.8059	-0.0126	0.1205	-0.0332	-0.08	-0.0138	0.1743	0.033	-0.0475	0.0005	-0.0409	0.0002	0.0284	0.0137	-0.0057	-0.0173	0.0151	-0.0523	-42.7417	-27.598	34.6526
12	0.5369	0.0954	-0.1152	1.0682	-0.188	0.6	-0.0674	-0.0406	-0.1207	-0.047	0.0087	-0.1422	0.119	-0.0809	0.0587	0.0052	0.0018	0.0045	-0.0439	0.0113	-0.0085	-33.8963	-39.4472	25.2875
13	0.5836	1.6289	-0.0986	6.4316	-0.2961	0.3022	0.0089	-0.0821	0.0357	-0.164	-0.0628	0.1104	0.0377	-0.0174	0.0539	-0.0122	0.0201	-0.0166	-0.0014	0.0077	-0.0411	-43.7621	-16.1448	25.041
14	1.5703	1.2059	-0.2338	1.8764	-0.3237	0.558	-0.0505	0.0284	0.1407	-0.0218	0.071	0.1534	0.0069	-0.0356	-0.0204	-0.0287	0.0282	-0.0145	-0.0109	-0.0127	-0.0313	-47.9913	-3.5012	21.7258
15	1.2271	1.3106	0.3752	1.217	0.3882	0.2697	-0.0242	-0.0465	0.0504	-0.0204	-0.0128	0.0348	0.0007	0.0018	0.037	0.0038	0.0147	-0.0102	-0.0024	-0.0058	0.0084	-41.4356	-9.1974	18.1226
16	1.6009	1.2064	0.7245	1.4038	0.503	0.856	-0.0288	-0.0406	-0.0431	-0.0375	-0.0001	-0.0342	-0.0039	-0.0111	0.0289	-0.0103	0.0214	-0.0015	-0.0276	-0.0048	-0.0141	-41.8276	-17.5766	16.677
17	1.9005	-0.1888	1.7071	0.3327	-0.1966	0.9866	0.0504	-0.3393	-0.0996	0.0258	0.0324	0.0487	0.1628	-0.2235	-0.0828	-0.0086	-0.0057	0.0013	0.0352	0.0068	0.003	-73.5929	-15.6138	19.1372
18	0.2929	-0.6466	0.0963	0.3359	-0.2357	1.4498	0.0626	0.1876	-0.0157	-0.034	-0.0138	0.1709	-0.0283	-0.1745	-0.0488	-0.049	-0.0153	-0.0073	-0.0046	-0.0279	-0.0288	-80.5678	-5.3552	0.4443
19	0.8241	0.0231	-0.1002	0.4381	-0.2341	0.1482	0.006	-0.1488	0.0172	0.1056	0.0214	0.0372	-0.0156	-0.0263	-0.0274	-0.0289	0.0114	-0.0001	0.0075	-0.0225	-0.0256	-77.7455	3.1112	15.6976
20	1.4256	-0.0585	-0.3448	0.8116	-0.0314	0.5528	0.0944	-0.1962	0.345	0.0615	-0.0262	-0.0313	-0.1266	-0.0035	-0.0682	-0.0436	0.0103	-0.0024	-0.0389	-0.0563	0.0403	-74.5606	19.5483	10.7466
21	0.8369	-1.0739	-0.8615	3.4295	2.1199	1.5203	0.0095	-0.086	0.0955	0.0796	0.0639	-0.1619	0.0716	-0.0144	-0.0734	-0.0272	0.0034	-0.0149	-0.0216	-0.015	-0.0228	-65.0133	-3.9482	11.4142
22	0.5713	-0.3416	-0.7474	0.8944	1.105	2.7634	-0.0726	-0.0848	-0.0106	0.0991	0.0825	-0.0402	0.1705	0.1596	-0.0099	-0.0168	0.0013	-0.0154	-0.0191	0.0044	-0.019	-57.1015	-15.2029	10.1235
23	0.1756	0.1073	-0.0659	0.3291	0.8902	1.8926	0.0341	-0.0053	0.0269	0.0132	0.049	-0.1044	0.0449	-0.068	-0.0831	0.0147	0.0091	-0.0141	-0.0039	-0.005	0.0061	-57.0693	-6.8315	5.9504
24	0.4908	0.1237	0.1789	0.1406	0.349	1.0147	-0.0531	0.0088	0.051	-0.0256	0.0128	0.0239	-0.0476	0.0334	0.0403	-0.0048	0.011	-0.0132	-0.0222	-0.0072	-0.0122	-57.6562	0.8374	9.9586
25	2.3704	-1.4919	1.2009	1.2437	-0.5446	0.9131	-0.0239	0.1639	0.2379	-0.0655	-0.0614	-0.1616	-0.0321	0.2221	0.0853	0.0081	-0.0391	0.0062	0.0153	0.0334	-0.0253	-35.7207	8.6736	-22.8915
26	1.4654	-0.0753	0.0161	0.5719	0.4954	0.8876	-0.0508	0.0928	0.0827	-0.1261	-0.0331	0.0624	-0.1199	-0.1719	0.0839	0.0293	-0.0045	-0.0143	-0.0324	0.0101	-0.0346	-57.7851	5.8011	-26.1034
27	0.0503	0.086	0.0416	0.0492	0.0253	0.2378	-0.0396	0.0752	-0.0182	-0.0699	0.0183	-0.0537	-0.0399	0.0639	0.0212	0.0265	-0.0232	0.0125	0.0136	-0.0074	-0.0313	-45.547	-6.4699	-29.9983
28	0.6527	-0.145	-0.1734	0.785	0.2516	0.962	-0.0416	0.0857	-0.1299	-0.032	-0.0387	-0.0278	0.1155	0.0233	0.0803	-0.0108	-0.0176	0.021	-0.0302	-0.0271	-0.0352	-54.6295	-21.4196	-29.4851
29	0.5002	-1.0537	-0.7728	3.3682	2.4429	2.1272	-0.0071	0.089	0.0332	0.0169	0.0323	-0.1199	0.0694	0.0286	-0.0252	-0.0017	-0.014	-0.0033	0.0027	0.0046	-0.0075	-44.5385	-2.8528	-15.3991
30	1.6574	-0.95	-1.134	1.1626	0.981	1.5059	-0.0397	-0.0468	0.0811	-0.0018	0.0785	-0.0917	0.0004	0.1086	-0.0388	-0.0367	-0.0128	-0.0243	-0.0421	0.0117	-0.0185	-40.4197	5.4385	-5.0476
31	0.57	-0.47	-0.079	0.6658	-0.0833	0.0416	-0.0026	0.0906	0.1087	0.0237	0.0001	-0.1007	0.0208	-0.0349	0.0025	0.0035	-0.006	-0.016	-0.0046	-0.0053	0.0104	-46.8823	-1.3307	-5.7176
32	1.6115	-1.1266	0.0928	1.5346	-0.0474	0.4774	-0.0322	0.072	-0.0495	0.0037	0.0107	-0.001	0.015	0.0072	0.0215	0.0016	-0.0194	-0.0047	-0.0155	-0.0086	-0.0291	-46.5925	-8.9702	-9.5035

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|10 - 33}
2	X-RAY DIFFRACTION	2	{A\|34 - 58}
3	X-RAY DIFFRACTION	3	{A\|59 - 143}
4	X-RAY DIFFRACTION	4	{A\|144 - 243}
5	X-RAY DIFFRACTION	5	{A\|244 - 278}
6	X-RAY DIFFRACTION	6	{A\|279 - 325}
7	X-RAY DIFFRACTION	7	{A\|326 - 356}
8	X-RAY DIFFRACTION	8	{A\|357 - 396}
9	X-RAY DIFFRACTION	9	{B\|10 - 33}
10	X-RAY DIFFRACTION	10	{B\|34 - 58}
11	X-RAY DIFFRACTION	11	{B\|59 - 143}
12	X-RAY DIFFRACTION	12	{B\|144 - 243}
13	X-RAY DIFFRACTION	13	{B\|244 - 278}
14	X-RAY DIFFRACTION	14	{B\|279 - 325}
15	X-RAY DIFFRACTION	15	{B\|326 - 356}
16	X-RAY DIFFRACTION	16	{B\|357 - 395}
17	X-RAY DIFFRACTION	17	{C\|10 - 33}
18	X-RAY DIFFRACTION	18	{C\|34 - 58}
19	X-RAY DIFFRACTION	19	{C\|59 - 143}
20	X-RAY DIFFRACTION	20	{C\|144 - 243}
21	X-RAY DIFFRACTION	21	{C\|244 - 278}
22	X-RAY DIFFRACTION	22	{C\|279 - 325}
23	X-RAY DIFFRACTION	23	{C\|326 - 356}
24	X-RAY DIFFRACTION	24	{C\|357 - 396}
25	X-RAY DIFFRACTION	25	{D\|10 - 33}
26	X-RAY DIFFRACTION	26	{D\|34 - 58}
27	X-RAY DIFFRACTION	27	{D\|59 - 143}
28	X-RAY DIFFRACTION	28	{D\|144 - 243}
29	X-RAY DIFFRACTION	29	{D\|244 - 278}
30	X-RAY DIFFRACTION	30	{D\|279 - 325}
31	X-RAY DIFFRACTION	31	{D\|326 - 356}
32	X-RAY DIFFRACTION	32	{D\|357 - 395}

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi