PDB-28jk: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-...

ID or keywords:

Entry

Database: PDB / ID: 28jk

Title

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 COMPLEXED WITH 3R-HYDROXY-4E-DECENOYL-CoA AND REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE

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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

Kiema, T.-R. / Wierenga, R.K. / Sirdhar, 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 5, 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	28jk.cif.gz	735.8 KB	Display	PDBx/mmCIF format
PDB format	pdb28jk.ent.gz		Display	PDB format
PDBx/mmJSON format	28jk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/8j/28jk ftp://data.pdbj.org/pub/pdb/validation_reports/8j/28jk	HTTPS FTP

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Related structure data

Related structure data	28jjC 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) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase 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)	65.285, 126.869, 225.342
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: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 716 / Label seq-ID: 21 - 736

Dom-ID
1
2

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

#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: The following regions were not modeled due to the disorder: Chain A residues: N353-GQA-S357 and L722 Chain B residues: Q352- NGQAS -A358, and H718-GSK-L722 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
#2: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂
#3: 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.: 2 / Source method: obtained synthetically / Formula: C₃₁H₅₂N₇O₁₈P₃S / 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H₂O
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: 57.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 100 mM MES, pH 6, 17 % w/v Polyethylene glycol 4000, 150 mM Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.92 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2023 / Details: Kirkpatrick-Baez mirror pair
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 2.29→49.275 Å / Num. obs: 84773 / % possible obs: 99.8 % / Redundancy: 13.4 % / B_iso Wilson estimate: 54.6 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.089 / Net I/σ(I): 19.9
Reflection shell	Resolution: 2.29→2.33 Å / R_merge(I) obs: 1.5 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4329 / CC_1/2: 0.621

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS	Jun 30, 2023	data reduction
XDS	Jun 30, 2023	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.44→49.275 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.951 / SU B: 15.239 / SU ML: 0.166 / Cross valid method: FREE R-VALUE / ESU R: 0.313 / ESU R Free: 0.212
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2068	3539	5.012 %
R_work	0.1736	67071	-
all	0.175	-	-
obs	-	70610	99.943 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 71.548 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.077 Å²	-0 Å²	0 Å²
2-	-	3.257 Å²	-0 Å²
3-	-	-	1.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.44→49.275 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10979	0	223	179	11381

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	11467
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	11089
X-RAY DIFFRACTION	r_angle_refined_deg	1.435	1.848	15562
X-RAY DIFFRACTION	r_angle_other_deg	0.669	1.763	25606
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.953	5	1426
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.214	5	90
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.418	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.479	10	1923
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.965	10	445
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1733
X-RAY DIFFRACTION	r_chiral_restr_other	2.141	0.2	28
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	13278
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2522
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	2319
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	9909
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	5652
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	5845
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	306
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.199	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	2.552	3.955	5710
X-RAY DIFFRACTION	r_mcbond_other	2.552	3.955	5710
X-RAY DIFFRACTION	r_mcangle_it	3.721	7.113	7131
X-RAY DIFFRACTION	r_mcangle_other	3.721	7.113	7132
X-RAY DIFFRACTION	r_scbond_it	3.8	4.476	5757
X-RAY DIFFRACTION	r_scbond_other	3.751	4.465	5746
X-RAY DIFFRACTION	r_scangle_it	5.722	8.079	8430
X-RAY DIFFRACTION	r_scangle_other	5.662	8.061	8413
X-RAY DIFFRACTION	r_lrange_it	7.317	39.839	12529
X-RAY DIFFRACTION	r_lrange_other	7.31	39.827	12510
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.086	0.05	22708

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	0.08639	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08639	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
2.44-2.503	0.284	242	0.238	4912	0.24	5157	0.948	0.965	99.9418	0.209
2.503-2.572	0.263	252	0.228	4721	0.23	4977	0.959	0.968	99.9196	0.196
2.572-2.646	0.258	266	0.215	4635	0.218	4903	0.962	0.974	99.9592	0.183
2.646-2.727	0.217	234	0.215	4493	0.215	4730	0.971	0.975	99.9366	0.181
2.727-2.816	0.24	217	0.206	4395	0.208	4612	0.966	0.978	100	0.173
2.816-2.915	0.24	216	0.205	4211	0.207	4428	0.966	0.976	99.9774	0.174
2.915-3.024	0.256	229	0.203	4077	0.205	4307	0.956	0.975	99.9768	0.172
3.024-3.147	0.254	226	0.198	3932	0.202	4158	0.964	0.976	100	0.17
3.147-3.287	0.213	216	0.197	3776	0.198	3993	0.968	0.976	99.975	0.172
3.287-3.446	0.227	184	0.193	3647	0.194	3833	0.964	0.978	99.9478	0.174
3.446-3.632	0.208	168	0.182	3476	0.183	3645	0.974	0.983	99.9726	0.169
3.632-3.851	0.2	187	0.171	3261	0.173	3448	0.978	0.985	100	0.161
3.851-4.115	0.193	166	0.158	3088	0.16	3255	0.977	0.986	99.9693	0.151
4.115-4.442	0.166	145	0.145	2885	0.146	3030	0.985	0.988	100	0.143
4.442-4.862	0.195	132	0.139	2683	0.142	2816	0.979	0.988	99.9645	0.141
4.862-5.429	0.188	115	0.159	2467	0.16	2582	0.979	0.987	100	0.161
5.429-6.257	0.187	106	0.171	2154	0.172	2260	0.981	0.985	100	0.173
6.257-7.632	0.203	108	0.163	1856	0.165	1964	0.975	0.985	100	0.174
7.632-10.666	0.16	94	0.117	1471	0.119	1567	0.984	0.991	99.8724	0.136
10.666-49.275	0.2	35	0.192	916	0.193	955	0.973	0.974	99.5812	0.236

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	2.5013	-0.5647	-0.2574	0.925	0.3814	0.802	-0.0334	-0.1347	0.2065	0.0062	-0.0076	0.0603	-0.0055	-0.0457	0.0411	0.1966	-0.0243	-0.012	0.0203	-0.0138	0.0337	-5.912	-9.446	2.348
2	5.3528	-0.4273	0.5563	2.1632	0.6869	3.7568	-0.028	0.9608	1.41	-0.6707	0.0306	0.0056	-0.908	-0.0089	-0.0027	0.5858	0.0054	0.0195	0.1934	0.2941	0.468	27.173	5.595	-17.892
3	0.9626	0.0971	-0.2542	1.0492	-0.5716	2.7186	-0.0646	0.2093	-0.1319	-0.3008	0.0055	-0.0394	0.2079	0.0373	0.059	0.2747	-0.0178	0.0215	0.0492	-0.0282	0.0189	29.591	-22.726	-22.899
4	4.16	-1.6336	1.9042	2.4741	-0.6752	2.2884	0.2721	-0.4666	-0.9507	-0.0887	0.1566	0.6605	0.4694	-0.1532	-0.4287	0.3518	0.0049	-0.0589	0.1378	0.205	0.3927	9.395	-13.339	-94.234
5	2.7896	1.0695	-1.2532	3.0271	-1.8111	6.2791	0.1749	-0.1772	-0.3983	-0.4176	-0.3602	-0.0138	1.4799	-0.0594	0.1854	0.902	0.0741	-0.1206	0.0948	0.018	0.1939	27.461	-34.297	-64.871
6	0.7084	-0.0764	0.0684	1.4798	-1.5909	4.4554	0.1503	0.0533	0.1092	0.3265	-0.4655	-0.1189	-0.1964	0.9075	0.3153	0.4034	-0.0279	-0.0803	0.2888	0.1389	0.1598	42.521	-8.272	-64.519

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 - 352
3	X-RAY DIFFRACTION	2	ALL	A	358 - 478
4	X-RAY DIFFRACTION	3	ALL	A	479 - 721

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