PDB-28jj: Crystal structure of rat peroxisomal multifunctional enzyme type-...

ID or keywords:

Entry

Database: PDB / ID: 28jj

Title

Crystal structure of rat peroxisomal multifunctional enzyme type-1 complexed with 2E,4E-decadienoyl-CoA, 3R-hydroxy-4E-decenoyl-CoA and NAD

Components

Peroxisomal bifunctional enzyme

Keywords

OXIDOREDUCTASE / hydratase / dehydrogenase / metabolism / fatty acid / CoA / beta oxidation / crotonase fold

Function / homology

Function and homology information

Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / fatty acid beta-oxidation using acyl-CoA oxidase / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / 3-hydroxyacyl-CoA dehydratase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Kiema, T.-R. / Wierenga, R.K. / Sridhar, S.

Funding support

1items

Citation

Journal: J.Struct.Biol. / Year: 2026
Title: Structural enzymological studies of multifunctional enzyme, type-1 (MFE1) with the 2E-decenoyl-CoA and 2E,4E-decadienoyl-CoA substrates: The regeneration of the dehydrogenase catalytic site is ...
Authors: Sridhar, S. / Schmitz, W. / Widersten, M. / Wierenga, R.K. / Kiema, T.R.

History

Deposition	Feb 3, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 22, 2026	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2026	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	28jj.cif.gz	729.4 KB	Display	PDBx/mmCIF format
PDB format	pdb28jj.ent.gz		Display	PDB format
PDBx/mmJSON format	28jj.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/8j/28jj ftp://data.pdbj.org/pub/pdb/validation_reports/8j/28jj	HTTPS FTP

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Related structure data

Related structure data	28jkC C: citing same article (ref.)
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	#127 - Jul 2010 Crystallins similarity (7) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Peroxisomal bifunctional enzyme

B: Peroxisomal bifunctional enzyme

hetero molecules

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

1

A: Peroxisomal bifunctional enzyme

hetero molecules

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

2

B: Peroxisomal bifunctional enzyme

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.481, 126.719, 226.168
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 717 / Label seq-ID: 21 - 737

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AB

#1: Protein	Peroxisomal bifunctional enzyme / PBE / PBFE / Multifunctional enzyme 1 / MFE1 / Multifunctional protein 1 / MFP1 Mass: 80959.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Lysine 514 to Arginine mutation / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ehhadh, Mfe1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P07896, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase

#1: Protein

Peroxisomal bifunctional enzyme / PBE / PBFE / Multifunctional enzyme 1 / MFE1 / Multifunctional protein 1 / MFP1

Mass: 80959.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Lysine 514 to Arginine mutation / Source: (gene. exp.)

Rattus norvegicus (Norway rat) / Gene: Ehhadh, Mfe1 / Plasmid: pET15b / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07896, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase

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Non-polymers , 6 types, 179 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-A1JZN / 2E,4E-decadienoyl-CoA / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (2~{E},4~{E})-deca-2,4-dienethioate Mass: 917.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₁H₅₀N₇O₁₇P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-A1JZ1 / (S)-3-HYDROXY-(E)-4-DECENOYL-COA / S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (E,3R)-3-oxidanyldec-4-enethioate Mass: 935.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₁H₅₂N₇O₁₈P₃S / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 125 mM MES, pH 6; 17 %w/v Polyethylene glycol 4000; 175 mM Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5418 Å
Detector	Type: Bruker PHOTON II / Detector: PIXEL / Date: Mar 26, 2020 / Details: Helios multilayer
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.1→64.798 Å / Num. obs: 110584 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 24 % / B_iso Wilson estimate: 27 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.291 / R_pim(I) all: 0.06 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 10.2 % / R_merge(I) obs: 2.4 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5357 / CC_1/2: 0.198 / R_pim(I) all: 0.773 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
SAINT	8.38A	data reduction
SADABS	2016/2	data scaling
PHASER	2.8.3	phasing
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→64.798 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.902 / SU B: 16.728 / SU ML: 0.192 / Cross valid method: FREE R-VALUE / ESU R: 0.294 / ESU R Free: 0.217
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2469	4221	4.998 %
R_work	0.2205	80240	-
all	0.222	-	-
obs	-	84461	99.844 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.576 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.494 Å²	0 Å²	0 Å²
2-	-	2.322 Å²	-0 Å²
3-	-	-	-1.829 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→64.798 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10915	0	228	171	11314

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	11409
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	11044
X-RAY DIFFRACTION	r_angle_refined_deg	1.457	1.847	15482
X-RAY DIFFRACTION	r_angle_other_deg	0.642	1.761	25498
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.056	5	1419
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.61	5	82
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.723	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.585	10	1913
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.745	10	441
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1726
X-RAY DIFFRACTION	r_chiral_restr_other	2.015	0.2	27
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	13187
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2511
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	2348
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	9940
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	5562
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	5755
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	282
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.238	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.166	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.638	0.941	5682
X-RAY DIFFRACTION	r_mcbond_other	0.638	0.941	5682
X-RAY DIFFRACTION	r_mcangle_it	1.117	1.691	7096
X-RAY DIFFRACTION	r_mcangle_other	1.117	1.691	7097
X-RAY DIFFRACTION	r_scbond_it	1.109	1.2	5727
X-RAY DIFFRACTION	r_scbond_other	1.068	1.189	5716
X-RAY DIFFRACTION	r_scangle_it	1.77	2.173	8385
X-RAY DIFFRACTION	r_scangle_other	1.703	2.152	8368
X-RAY DIFFRACTION	r_lrange_it	3.784	10.107	12482
X-RAY DIFFRACTION	r_lrange_other	3.772	10.1	12468
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.092	0.05	22276

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0925	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0925	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.3-2.36	0.324	303	0.317	5880	0.317	6183	0.924	0.929	100	0.294
2.36-2.424	0.309	280	0.294	5755	0.294	6035	0.931	0.94	100	0.268
2.424-2.494	0.299	268	0.281	5546	0.282	5815	0.943	0.947	99.9828	0.252
2.494-2.571	0.307	296	0.261	5375	0.264	5672	0.94	0.954	99.9824	0.232
2.571-2.655	0.279	282	0.247	5220	0.248	5502	0.947	0.959	100	0.218
2.655-2.748	0.272	274	0.244	5106	0.246	5380	0.949	0.96	100	0.213
2.748-2.852	0.277	258	0.242	4924	0.243	5182	0.944	0.961	100	0.21
2.852-2.968	0.271	226	0.232	4736	0.233	4962	0.948	0.964	100	0.202
2.968-3.1	0.282	231	0.235	4542	0.237	4773	0.946	0.963	100	0.206
3.1-3.251	0.26	226	0.231	4347	0.233	4577	0.949	0.965	99.9126	0.203
3.251-3.426	0.261	230	0.225	4125	0.227	4360	0.957	0.968	99.8853	0.2
3.426-3.633	0.233	198	0.222	3943	0.223	4148	0.966	0.971	99.8312	0.203
3.633-3.883	0.234	213	0.206	3664	0.207	3881	0.963	0.973	99.8969	0.189
3.883-4.193	0.23	174	0.183	3444	0.186	3623	0.964	0.978	99.862	0.171
4.193-4.591	0.173	179	0.173	3193	0.173	3373	0.981	0.981	99.9704	0.164
4.591-5.13	0.19	158	0.171	2903	0.172	3070	0.978	0.982	99.7068	0.164
5.13-5.917	0.232	144	0.188	2589	0.19	2733	0.971	0.981	100	0.176
5.917-7.232	0.231	134	0.187	2197	0.19	2331	0.972	0.98	100	0.177
7.232-10.165	0.156	88	0.138	1751	0.139	1840	0.987	0.989	99.9457	0.144
10.165-64.798	0.29	56	0.277	976	0.278	1123	0.964	0.961	91.8967	0.286

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	2.9794	0.6994	-0.5749	1.3451	-0.6057	1.1115	-0.0249	0.1238	0.1821	-0.0274	-0.0193	-0.1001	-0.0488	0.0696	0.0443	0.0859	0.0027	-0.0164	0.0149	0.0083	0.2811	-26.906	-9.486	-2.161
2	3.853	-0.4998	0.7033	2.7823	-0.5891	5.8895	-0.1712	-0.7626	1.1658	0.7279	0.1496	-0.085	-1.0695	0.0886	0.0216	0.5555	0.0047	0.0263	0.1619	-0.2376	0.6523	-60.273	5.635	17.887
3	0.9395	-0.0743	-0.3969	1.382	0.4608	3.5697	-0.0675	-0.2335	-0.0956	0.4157	0.0333	0.08	0.2057	-0.098	0.0342	0.1853	0.0289	0.0431	0.0726	0.0294	0.2618	-62.455	-22.654	23.158
4	4.2376	1.1712	2.288	2.978	1.1229	2.7526	0.3078	0.3676	-0.8111	0.2006	0.1459	-0.5696	0.5125	0.1258	-0.4537	0.2463	-0.0083	-0.0611	0.0707	-0.1774	0.5121	-41.956	-13.262	94.491
5	3.2787	-1.2717	-1.5243	2.9694	0.9403	6.5675	0.2384	0.201	-0.3539	0.2412	-0.3519	0.0018	1.3668	0.151	0.1136	0.9468	-0.0479	-0.1182	0.0822	-0.0556	0.4577	-60.358	-34.546	65.03
6	0.8022	0.0309	-0.0666	1.6067	1.2494	5.3401	0.173	-0.0037	0.1216	-0.3306	-0.3776	0.0534	-0.0761	-0.8733	0.2046	0.3061	0.0063	-0.0591	0.2145	-0.1235	0.3728	-75.116	-8.251	64.767

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 275
2	X-RAY DIFFRACTION	2	ALL	A	276 - 350
3	X-RAY DIFFRACTION	2	ALL	A	357 - 478
4	X-RAY DIFFRACTION	3	ALL	A	479 - 720

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